STN Express with Discover! 6.0 User Guide - STN International

STN Express 

with Discover! 6.0 

User Guide 

for Windows 

Version 6.0 

April, 2001 

Copyright Ó 2001 American Chemical Society 

All rights reserved.

1 

Introduction 

Introduction 1–1 

Overview of 


6.0 

STN Express with Discover! is a fully integrated software package 

designed to easily and efficiently search scientific and technical 

databases online through STN as well as other online hosts. It includes: 

• a “wizard” interface for logon setup, selecting databases, conducting 

searches, displaying or analyzing results, creating and editing alerts, 

and much more, without having to know the STN command language 

• easy retrieval of data for hyperlinked CAS Registry Numbers®, 

patent numbers, and other information 

• post-processing options for creating reports and tables from 

transcripts 

• easy access to Web services through your Web browser 

• easy structure-drawing and searching on STN 

• fragmentation code generation from query structures for searching in 

World Patent Index 

• convenient access to the STN command-line interface. 

System 

Requirements 

STN Express 6.0 with Discover! requires: 

Computer: 

an Intel 486 processor or compatible; a Pentium 

is recommended 

Connection to STN: a local modem, networked modem, or a TCP/IP 

(Internet) connection that supports the telnet 

protocol 

Operating System: Microsoft Windows 95, 98, Me, NT 3.51, NT 4.0 

or 2000 

Memory: 

32 MB of RAM; 64MB is recommended 

Hard Drive: 

16 MB or more of free hard disk space 

Monitor: 

VGA color monitor compatible with Windows, 

800X600 minimum screen resolution 

Mouse: 

a mouse, trackball, or similar pointing device 

Printer: 

high-quality graphics printer, e.g., laser or inkjet 

Internet: 

a web browser and Internet connection for those 

features that provide links to the World Wide 

Web

1–2 Introduction 

Help 

You have the following options for STN Express help: 

• select an option from the Help menu on the Main Menu bar 

• press F1 or click the Help buttons for context-sensitive help. 

Technical Support 

For technical assistance, please consult Appendix I, Troubleshooting, in 

your User Guide or visit http://www.cas.org/Support/software.html on the 

World Wide Web. If you continue to experience problems, contact your 

Help Desk by email or telephone. To send email, you may go to the STN 

Express Help menu, select Request Help…, and then choose your STN 

Service Center to open your email application. 

North America 

(and areas not in Japan or Europe) 

CAS 

2540 Olentangy River Road 

P.O. Box 3012 

Columbus, OH 43210-0012 USA 

Phone: 800-848-6533 (North America) 

614-447-3698 (worldwide) 

Fax: 614-447-3798 

Email: help@cas.org 

WWW: http://www.cas.org 

Japan 

Japan Science and Technology Corporation (JST) 

5-3 Yonbancho Chiyoda-ku 

Tokyo 102-0081 Japan 

Phone: (03) 5214-8414 

Telefax: (03) 5214-8410 

E-mail: overseas@mr.jst.go.jp 

WWW: http://www.jst.go.jp 

Japan Association for International Chemical Information (JAICI) 

Nakai Building 

6-25-4 Honkomagome, Bunkyo-ku 

Tokyo 113, Japan 

Phone: (03) 5978-3601 

Fax: (03) 5978-3600 

Email: helpdesk@jaici.or.jp 

WWW: http://www.jaici.or.jp/

Introduction 1–3 

Europe 

STN International 

c/o FIZ Karlsruhe 

P.O. Box 2465 

D-76012 Karlsruhe Germany 

Phone: +49-7247/808-555 

Fax: +49-7247/808-259 

Email: hlpdeskk@fiz-karlsruhe.de 

WWW: http://www.fiz-karlsruhe.de/ 

About this User 

Guide 

The user guide covers both the basic and the advanced features of STN 

Express with Discover! 6.0. 

You should be familiar with your Windows operating system. If you are 

not, you may refer to your owner’s guide for detailed information on your 

system. 

Items that you select, e.g., STN Express buttons or menu options, are 

presented in bold type. 

Information intended for you to type or titles of publications or chapters 

are presented in italics.

2 

Installation and Main Menu 2–1 

Installation and Main Menu 

Installation 

This chapter covers the following topics 

• Installing from CD-ROM 

• Upgrading to STN Express 6.0 with Discover! 

• Installing Adobe Acrobat Reader 

• Installing QuickTime 

• Opening STN Express with Discover! 

• Main Menu and Toolbar 

For information on Network Installation, refer to Appendix G. Network 

Installation, of your electronic STN Express with Discover! User Guide or 

the ReadMe.txt file. 

Installing from 

CD-ROM 

1. Insert the STN Express with Discover! CD-ROM into the CD-ROM 

drive to start the STN Express setup program. 

If the setup program does not automatically start, double-click the 

CD-ROM icon to open it and then double-click setup.exe. 

2. Install STN Express with Discover! dialog box is displayed.

2–2 Installation and Main Menu 

Select any or all of the following in the Setup Options: 

• Copy Software to HD - to install the STN Express with Discover! 

software 

• Softcopy documentation - to install the electronic STN Express 

User Guide 

• Start Menu Item - to create a Windows Start Menu item for STN 

Express 

Select the appropriate Setup Type: 

• Single User - to install STN Express with Discover! to your local hard 

drive 

• Network User - see your Network Administrator for details 

• Network Server - for information, refer to Appendix G, Network 

Installation in the STN Express User Guide or click the View ReadMe 

button to view the ReadMe.txt file. 

Click Install STN Express with Discover!. Respond to the prompts to 

complete installation. 

Upgrading to 

STN Express 6.0 


drive to start the STN Express setup program. 

2. Choose your setup options and select Single User from the Setup 

Type. 

3. Click Install STN Express. 

Because you have an existing copy of STN Express, its current 

location is placed in the dialog box as the default. Click Yes to 

overwrite your existing copy of STN Express. 

Note that only files provided by your previous STN Express 

installation programs are overwritten. Any structures, scripts, 

transcripts, and logon setups that you have created are retained. 

4. Respond to the prompts to complete installation. 

Installing Adobe ® 

Acrobat ® Reader 

The STN Express with Discover! User Guide is a PDF file. You will need 

Adobe Acrobat Reader to view the User Guide. To install the Acrobat 

Reader 4 from the STN Express with Discover! CD-ROM, follow these 

steps: 


drive. 

2. Click the Install Adobe Acrobat Reader button. 

3. Respond to the prompts to complete the installation.


Installing 

QuickTime 

QuickTime 4 software is needed to display JPEG (.jpg) and GIF (.gif) 

images that can be downloaded in some STN files. 


drive. 

2. Click the Install QuickTime button. 

3. Respond to the prompts to complete the installation. 

Opening STN 

Express with 

Discover! 

To open STN Express with Discover! 

1. Launch STN Express with Discover! from the Windows Start menu. 

By default, an entry has been made under Programs. 

2. When STN Express with Discover! is open, the STN Express Main 

Menu & Toolbar are displayed. 

Main Menu 

The Main Menu contains the following menus: 

• File 

• Logon 

• Query 

• Results 

• Setup 

• Web 

• Help 

File menu 

File menu item 

Edit Text File 

Exit STN Express 

Function 

Edit a text file, such as a script 

Close the STN Express application 

and all associated applications


Logon menu 

The Logon! allows you to connect to an online service via a logon setup. 

There are no sub-menus to Logon!. 

Query menu 

The Query menu provides commands to build, edit, or use chemical 

structure queries, command files, predefined search strategies, and WPI 

fragmentation code strategies. For details, refer to Chapters 6-9. 

Query menu item 

Prepare Structure Query 

Prepare Command File 

Check Command File 

Edit WPI Strategy 

Generate WPI Strategy 

Print WPI Strategy 

Include WPI Other Code 

Concepts 

Function 

Open a new “Standard” structure 

drawing window. 

Open a file to create a script of 

commands for your online session. 

Refer to Appendix C for details. 

Check a script for errors. 

Edit an existing Derwent WPI 

fragmentation code strategy. Refer to 

Chapter 8 for information. 

Generate a WPI fragmentation code 

strategy for a WPI query structure. 

Refer to Chapter 8 for information. 

Print a WPI fragmentation code 

search strategy. 

Select Other Code Concepts to 

include when generating a WPI 

fragmentation code strategy. Refer to 

Chapter 8 for more information.


Results menu 

Results Menu Item 

Browse Transcript 

Print Transcript 

Edit Transcript 

Export Transcript 

Accounting 

Table Tool 

Report Tool 

Predefined Report 

Open 

Function 

Open (display) a transcript in Browse 

mode. 

Print one or more transcripts. 

Edit the text portion of a .trn transcript. 

Export a transcript to a new RTF file. 

Create a cost report for STN online 

sessions. Refer to Chapter 12 for 

more information. 

Create a table from search results in 

transcript. 

Create a custom report from search 

results in transcripts. 

Create a predefined report from 

patent search results in transcripts. 

Open the Trnscrpt folder to browse 

transcripts, reports, and tables 

Setup menu 

Setup Menu Item 

STN Setup Wizard 

Connections 

Preferences 

Save Configuration 

Restore Saved Configuration 

Function 

Create an automated logon setup. 

Create or modify a logon setup 

configuration for an online host. 

Customize Preferences. Refer to 

Appendix A for information on General 

and STN Online and Results 

Preferences. Refer to Chapter 6 for 

information on Structure Drawing 

preferences. 

Save all logon setups. 

Restore all logon setups to the last 

saved configuration.


Web menu 

Web Menu Item 

STN Columbus 

STN Karlsruhe 

STN Tokyo 

Function 

Link web browser to STN Columbus 

services. 

Link web browser to STN Karlsruhe 

services. 

Link web browser to STN Tokyo 

services. 

Help menu 

Help Menu Item 

Index 

Using Help 

View STN Express User Guide 

About STN Express 

Function 

Obtain an index of help for STN 

Express. 

Find out how to use Windows help. 

Open the STN Express User Guide in 

your Adobe Acrobat Reader. 

View copyright and version 

information.


Main Toolbar 

The Toolbar is used to quickly open the STN Express applications. 

Tool Button Name 

Setup 

Logon 

Prepare Query 

Browse Transcript 

Print Transcript 

Table Tool 

Custom Report Tool 

Predefined Report 


Preferences 

Help 

Exit 

Function 

Create logon setups 

Log onto an online service 

Open a structure drawing window 

Open transcript and other files 

Print transcript and other files 

Create tables from transcript search 

results 

Create custom reports from 

transcripts 

Create a patent report from transcripts 

using a predefined template 

Open a transcript file for editing 

Set preferences 

Display a list of help topics. 

Quit the STN Express applications.


Customizing 

the Toolbar 

To replace a button or gap on the Toolbar, follow these steps: 

1. Right click on a button or in an empty space on the toolbar. 

2. The STN Express Toolbar Preferences dialog box is displayed. 

Click Next.


3. Click the Next button until the icon for the desired tool appears. Click 

OK to complete the action and select the button. 

4. The new button appears on the toolbar.


To remove a tool button from the Toolbar, follow these steps: 

1. Right-click on the tool button that you want to remove. 

2. Click OK in the STN Express Toolbar Preferences dialog box.

3 

STN Logon Setup 

STN Logon Setup 3–1 

Your online connection and logon information are required each time you 

connect to STN or another online host. This information, e.g., the 

telephone number your modem will dial, or the Internet address of the 

host, is stored in a logon setup. 

For the latest logon setup information, visit 

http://www.cas.org/Support/software.html 

This chapter includes description and examples of the following topics on 

STN logon setups: 

• Internet setup with STN Setup Wizard 

• Manual modem setup 

• Customizing for academic accounts 

• Setup Definition Values 

• Managing setups 

Internet Setup 

with STN 

Setup Wizard 

If you do not have any logon setups, the STN Setup wizard starts when 

you launch STN Express. 

You may also access the wizard via the Setup menu. 

Click the Before I Begin button on the opening page for details of how to 

use the wizard.

3–2 STN Logon Setup 

Follow these steps: 

1. Select the STN Service Center for your account and confirm your 

STN Logon Port. For commercial accounts, X is usually correct. For 

other accounts, consult the materials supplied with your STN login ID. 

Click Next. 

2. Select the middle radio button to specify an Internet connection to 

STN.


3. Give your new logon setup a name by which you will remember it. If 

you choose, type your STN login ID and password to save them in the 

setup. Click Finish. 

Manual 

Modem Setup 

1. Click on the STN Express Toolbar. 

2. The STN Setup dialog box is displayed. Click New to create a new 

setup.


3. The Setup Definition dialog box is displayed. 

Enter or select the following information: 

• type a name in Setup Name 

• select your STN Service Center, e.g., STN-Columbus, from the Host 

Name pull-down menu 

• type your Login ID and password (optional) if you do not want to be 

prompted for them at login 

• select your modem or appropriate communication option in Connect 

Via 

• for the Logon Method, select the appropriate telecommunications 

network or Directdial from the Standard list. 

Some telecommunications networks require additional information, 

i.e., Network User Address, Network User ID, Network User 

Password. If required, a Network Logon section is added into this 

dialog box. Enter the appropriate information. 

• In the Primary Phone # box, type the telephone number appropriate 

for your Logon Method 

• select Standard as the Logoff Method 

Click OK. 

If you entered your password, you are prompted to re-enter it for 

verification. After you re-enter it, click OK.


4. Click Save to save this setup to your hard disk. Click OK to return to 

the STN Express Main Menu & Toolbar. 

Customizing 

for Academic 

Accounts 

If you have an academic account, you need to change: 

• STN Port in logon setup 

• Account Preferences


Changing STN 

Port with STN 

Setup Wizard 

If you are using the STN Setup Wizard, replace the Logon Port of X with 

the appropriate academic account port for your area. Contact your STN 

account administrator or your STN Service Center for this information.


Changing STN 

Port in a Manual 

Logon Setup 

1. Click on the STN Express Toolbar. Highlight the setup you want 

to modify. Click Modify. The setup Definition dialog box is displayed. 

Click the Host Settings tab. 

2. Replace the STN Port of X with the appropriate academic port for 

your area.


Changing Account 

Preferences 

for academic 

accounts 

To customize Account Preferences for academic accounts, follow these 

steps: 

1. Click Setup from the Main Menu. Select Preferences and then 

STN Online and Results. 

2. Click on the Account tab of Preferences. 

In the STN Account Type box, select the type of account you have and 

its features: 

• Commercial (Full access) - default setting 

• Full Academic - if you have access to STN files under your academic 

program 

• FIZ Academic - if you have access to FIZ discounted files only 

• CAS & FIZ Academic - if you have access only to CAS and FIZ files 

under your academic program 

• BEILSTEIN subscriber - if you have a Beilstein subscription 

• GMELIN subscriber - if you have a GMELIN subscription 

• DERWENT subscriber - if you have a DERWENT subscription 

Under Property Data Databases, select the property databases that the 

Discover! wizards are authorized to access. 

Click OK.


Setup 

Definition 

Values 

The Setup Definition dialog box opens when you click New or Modify 

buttons in the STN Setup dialog. This dialog box contains the logon setup’s 

settings, including the name of the online host and the details about how to 

connect to the host. 

Setup name 

The Setup Name identifies a specific setup. The name must be 20 

characters or fewer and can include any combination of letters, numbers, 

special characters, and spaces. 

Suggested setup names would help identify the host, e.g., STN, and the 

connection method, e.g., Internet. 

Host name 

The Host Name identifies the online host that you want to access in this 

setup. Select the STN Service Centers for your account from the Host 

Name pop-up menu 

Login ID 

Type your STN login ID in the Login ID box. Entering a login ID at this 

time is optional. If you do not enter it here, you will be prompted to enter it 

when you log on to STN. 

Password 

Enter your STN password in the Password. For security, an asterisk is 

displayed for each password character you type. Your password is stored 

in the express.ini file in an encrypted form. Entering a password at this 

time is optional. If you do not enter it here, you will be prompted to enter it 

when you log on to STN. 

Path 

Select Path 1 to define the first communication path to STN. Select Paths 

2-4, as needed, to define alternate communication paths. When STN 

Express tries to connect to STN, it first uses Path 1. If Path 1 fails to 

connect, STN Express tries the next path until the connection is made or 

there are no more paths to try.


Host Settings 

Select the Host Settings tab to see settings that are specific to STN. 

Many of the settings are critically important and cannot be changed. 

Click a √ in the Command Window box to cause STN Express with 

Discover! to open a Command Window when you log on to STN. The 

Command Window can be turned off and on while you are logged on. 

Click a √ in the Close Window at logoff box to tell STN Express with 

Discover! to close the session window after you log off. If you prefer to 

view cost information, scroll back through your session for any reason, or 

capture a transcript after you log off, do not select this option. 

Up to five commands may be entered in the Execute at first Host 

Prompt window. The first command is sent when the first => prompt is 

received, and the remaining commands are sent, one at a time, with each 

succeeding arrow prompt. 

By default, a carriage return is sent after each line. The keyword NOCR 

may be added as the last word on the last line that you enter to indicate 

that this line is to be displayed in the STN Online and Results window, 

but not sent. This allows you to enter data after the defined character 

string, before it is sent.


The STN Port is X by default and is a appropriate for commercial 

accounts. Change it to the port letter appropriate for you account if 

necessary. 

The Graphics option specifies whether chemical structure diagrams will 

be displayed in a transcript. Uncheck the Graphics box if you do not want 

to display structure graphics. 

Connect via 

Select a communication method from the Connect via pulldown menu to 

connect to the online host you selected. 

The method that you choose controls the information that is required in the 

Communication Settings section. This is described further in the 

Communications Settings section, later in this chapter. 

Connect via options are: 

• Winsock (Internet) - select if your network software supports 

Windows Sockets and Telnet from your PC (most do). When 

selected, the Host Name or IP Address, Port, and Echo fields are 

displayed. Enter the host name or host address, if different from 

the default (rare). Set Echo to No if you do not want STN Express 

with Discover! to echo characters as they are typed. The Port 

setting of 23 (Standard Telnet) in most cases should not be 

changed. 

• Dial-Up Networking - STN Express with Discover! lists all 

connections defined in Windows Dial-Up Networking. Dial-Up 

Networking connections are most commonly used to define 

connections to the Internet via an Internet Service Provider (ISP). 

When you log on to STN, STN Express with Discover! will attempt 

to use the Standard Windows interface to Dial-Up Networking (in 

WININET.DLL). You will be prompted to connect to your ISP as 

needed. NOTE: Winsock is the underlying connection type for 

this option. 

• Modem - STN Express with Discover! lists all modems installed in 

the Windows Modems Control Panel. This option eliminates the 

need to set many of the modem options, because this information 

is obtained directly from Windows. Most users will only need to 

specify a phone number for this option. NOTE: If you cannot 

make a connection using this method, try using COM port option. 

• COM1, COM2, COM3, or COM4 - select to connect via a serial 

port, e.g., to a modem, terminal server, or host system.


Standard logon 

Use a Standard Logon Method to connect to STN via one of the 

supported networks. 

To use a standard logon procedure, click the radio button next to 

Standard in the Logon Method section and select one of the supported 

networks from the pulldown menu. STN Express with Discover! 

automatically inserts the scripts to connect to STN through the selected 

network. 

For example, if a setup is defined to connect to STN-Karlsruhe via Datex- 

P, STN Express with Discover! selects several scripts from the Scripts 

folder: 

• a script that sends dial commands to a modem 

• a script that connects to STN-K via the Datex-P network. 

• a script that logs on to STN. 

The scripts use the values in the logon setup, such as dial method, phone 

number, and NUA, to make the connection and log you in. 

Standard logoff 

Click the radio button next to Standard in the Setup Definition dialog box 

to tell STN Express with Discover! to use the discnct script to disconnect 

the communication path. This script handles most connections, including 

those made through a modem and via Winsock. If STN Express with 

Discover! does not correctly disconnect the communication path, you will 

need to define a custom logoff. 

Network Logon 

The Network Logon section in the Setup Definition dialog box is 

displayed when STN Express with Discover! recognizes that the Connect 

via option you selected requires information to make the network 

connection to STN. You may need to enter any of the following values: 

• NUA (Network User Address) - the address of the host on the 

network you selected. The value may be a character string, e.g., 

stnc, or a numerical string, e.g., 03106001467 

• NUI (Network User Identifier) - a character string that identifies 

the user to the network. Some networks require this. 

• NUP (Network User Password) - a password to confirm the 

identity of the user on the network. Some networks require this. 

To keep the NUP entry secure, only asterisks are displayed when you 

type this value. It is stored in the express.ini file in encrypted form. To 

confirm your NUP, you are prompted to re-enter the password after you 

select OK in the Setup Definition dialog box. 

STN Express with Discover! provides the NUA values for a limited number 

of networks. If an NUA is not available, an error message is displayed 

when you try to use the setup. If this occurs, return to the Setup 

Definition dialog box. Then select the path that failed and fill in the NUA 

and related fields.


Communications 

Settings 

The Communications Settings section of the Setup Definition dialog 

box contains the communication parameters used by STN Express with 

Discover! to connect to a host. The available settings are based on your 

selection in the Connect via pulldown menu. 

Settings for Winsock (Internet) and dial-up networking setups 

An example logon setup for STN-Karlsruhe using the Internet is shown: 

The Communications Settings for STN logon setups when Connect via is 

Winsock (Internet) or a Dial-Up Networking item are 

• Host Name or IP Address - the name or address of the STN 

computer to which STN Express will connect. For example, the 

name of the STN-Karlsruhe computer is stnk.fiz-karlsruhe.de and 

its address is 141.66.16.239. These values are provided 

automatically when you select an STN Service Center from the 

Host Name list. 

If you must connect to STN through a telnet gateway, enter the 

name or IP address of the gateway and see Appendix F for more 

information. 

• Port - the TCP/IP port number for telnet (Winsock) connections. 

The default is 23, and you should change this only if your 

organization has a firewall that uses a different port for the telnet 

protocol.


• Echo – the duplex setting that specifies whether to echo 

characters as they are typed. If you cannot see the characters 

you are typing or if you see two characters for every one that you 

type, try changing the Echo selection. 

Settings for modem setups 

When the name of a modem is selected in Connect via, the following 

settings are available in STN Express. To view and change the modem’s 

other communications settings, use the Windows Modems Control Panel. 

• Echo – the duplex setting that specifies whether to echo 




• Break Length - the duration of a Break signal sent by STN 

Express with Discover! through a serial (modem) connection. The 

duration ranges from 10 to 2000 milliseconds; the default is 500. 

If STN does not recognize the Break signal, you may need to 

increase this value. If the Break signal disconnects you from your 

network, you may need to decrease this value. 

• Dial - the type of dialing to be used: Tone, Pulse (rotary), or 

Manual. If Manual is specified, STN Express with Discover! 

issues a message and waits for you to manually dial the 

telephone. 

• Primary Phone # - the telephone number for the network provider 

you selected. 

• Secondary Phone # - an alternate telephone number for your 

network provider that is used if the primary phone number fails to 

connect.


Settings for COM Port setups 

Here is an example logon setup for STN-Columbus using a COM port: 

When the COM port to which your modem is attached is selected in 

Connect via, the following settings are available in STN Express. 

· Echo - the duplex setting that specifies whether to echo 




· Break Length - the duration of a Break signal sent by STN 



If STN does not recognize the Break signal, you may need to 

increase this value. If the Break signal disconnects you from your 

network, you may need to decrease this value. 

· Speed (bps) - the serial port speed used to connect to your 

modem. The speed may range from 300 to 57600 bits per second. 

Select the highest speed that your modem supports.


· Flow Control - the type of flow control, e.g., None, Software 

(XON/XOFF), Hardware (RTS/CTS), to be used. Flow Control is 

used to prevent the overflow and loss of data from an online host. 

Hardware is the default and should be used in most cases. Data 

loss may occur if this setting is not synchronized with your 

modem’s settings. 

· Data bits, Stop bits, and Parity - select to identify the number of 

data bits in each byte sent or received, the minimum number of 

bits sent after each byte, and the parity. 8, 1.0, and NONE are 

nearly always the best choices and are the defaults. Use 7, 1.0, 

and EVEN when the maximum modem speed is lower than 9600 

baud. 

· Dial - the type of dialing to be used: Tone, Pulse (rotary), or 



telephone. 

· Primary Phone # - the telephone number for the network provider 

you selected. 

· Secondary Phone # - an alternate telephone number for your 

network provider that is used if the primary phone number fails to 

connect. 

Advanced (Communications Settings) 

The Advanced option in the Communications Settings section of the 

Setup Definition dialog box is used to provide information used by three 

different features of STN Express with Discover!. They are: 

· connecting to STN through a telnet gateway, firewall, or proxy 

server. Refer to Appendix F for details. 

· sending an initialization string to a modem 

· sending a character string instead of a standard Break command

Click the Advanced button to open the Advanced dialog box. 


Enter the appropriate information. Click OK when all specifications are 

entered. Or click Cancel to cancel all the specifications. 

Modem Configuration 

Enter values in the Modem Configuration section to define an 

Initialization String for the modem. If you specify a value in this field, 

the string is sent to the modem before the dial command is issued, 

and a response of OK is expected. See your modem manual for 

details about modem commands and options. NOTE: Not 

recommended if you have selected the name of your modem from the 

Connect via list. 

The Phone # field in the Modem Configuration section normally 

displays the value of the Primary Phone # for this path. For the 

special case when the phone number fields in the Communication 

Settings area are not available, e.g., for Winsock connections to a 

network modem pool, use this field to specify a telephone number. 

Other 

Enter the appropriate value in the Break sequence text box to define 

a character string that you want STN Express with Discover! to use as 

a Break indication to an online host. This value is needed only for 

systems that do not support a standard Break.


Custom Logon 

Use custom logon when STN Express does not support the network you 

choose, i.e., if the telecommunications network you use to connect to STN 

is not in the Logon Method Standard list. A custom logon method is also 

appropriate if you must use a combination of supported networks. 

A custom logon requires you to select scripts to tell STN Express with 

Discover! how to connect to STN. Scripts typically are used to execute a 

step in the logon process. For example, one script might have the modem 

dial a telephone number and connect to a telecommunications and 

network a second script may connect to STN through that network. Always 

use the STNLOGON script to log on to STN. 

You may also write your own script to connect through an unsupported 

network. For information on writing scripts, refer to Appendix C, Script 

Language. 

To create a custom logon procedure, click the radio button next to 

Custom in the Logon Method section. Then click the Configure button. 

The Custom Logon dialog box is displayed. 

The Scripts Folder box displays a list of scripts from either the User or 

Standard scripts folder. The Standard scripts folder corresponds to the 

Predefined Scripts folder in General Preferences. The User scripts 

folder corresponds to the User Scripts folder in General Preferences. 

The Selected script list box displays the scripts that have been selected 

for this custom logon setup. The scripts will be executed in the order 

shown as part of the connect and logon process. To change the order of 

the scripts in the Selected script list, select a script and click the up (▲) 

or down (▼) arrow to move the script name one position at a time.


To add a script to the logon procedure, select (highlight) a script in the 

Scripts Folder list. Then click the Copy>> button to copy the script to the 

Selected script list. Click the Watch Me button to insert the watchme.sc 

script into the Selected script list window. The watchme.sc script can be 

used more than once in the Selected script list. For more information, 

refer to the Watch Me section later in this chapter. 

Click the Delete button to delete a script from the Selected script list. 

Click the View button to display the actual script for a script name that you 

select from the Scripts Folder window. 

Click OK to when you have completed your entries to the Selected script 

list window and to return to the Setup Definition dialog box. The scripts 

you selected are displayed in the Custom Logon Script List box. 

Watch Me 

For some custom logon methods, a custom-written script is needed. You 

may write the script yourself, but it may be more efficient to let Watch Me 

write it for you. The Watch Me function creates a script by recording the 

commands that you enter from the keyboard and the network’s responses 

when you log on to a network. 

STN Express with Discover! begins the Watch Me function when it finds 

the script named watchme.sc as the name of the script that it is ready to 

execute. After watchme.sc is found, you are prompted to enter the name 

of the new script that is to be created. (After Watch Me has finished, 

watchme.sc is replaced with the new script in the Custom Logon Script 

List.) 

A dialog box with two buttons, Stop and Cancel is displayed. An STN 

Express with Discover! script is created in this window and is generated 

from the commands entered from the keyboard and from the prompts 

received from the host system. The script continues to be created until 

you click Stop. 

STN Express with Discover! continues executing the next script listed in 

the Selected scripts list window located in the Custom Logon dialog 

box. The next time you log on using this setup, your newly created script 

will run, executing the commands recorded during the Watch Me function. 

Click Cancel, at any time, to cancel the Watch Me function without 

creating the new script.


Custom logoff 

Use a custom logoff procedure when the method to disconnect from an 

online host is not successful or is not supported by the standard logoff 

method. 

The Logoff Method section in the Setup Definition dialog box defines 

how STN Express with Discover! will disconnect the communications path 

when you log off from an online host. 

When you log off, STN Express with Discover! scans the output from the 

host system looking for the logoff messages defined under the Host 

Settings tab in the Setup Definition dialog box. When it locates a 

message, STN Express with Discover! knows that is has logged off of the 

remote system. It then disconnects the communication path using the 

method defined in this section. 

☞ If the communication path is not disconnected correctly, you may get 

a “Communication Port In Use” error when you try to use a program 

that requires the use of a communication port. 

The steps for defining a custom logoff are nearly identical to that for 

defining a custom logon. Refer to Custom Logon in this chapter for 

details. 

Managing 

Setups 

Open the STN Setup dialog box by clicking the Setup button in the main 

toolbar or by clicking Setup | Connections.


Modifying a setup 

To modify an existing logon setup, select a setup from the Setup Names 

list in the STN Setup dialog box. Then click Modify. The Setup Definition 

dialog box is displayed, as well as the values you selected for this setup. 

Change any value. Then click OK to accept the changes or Cancel to 

cancel the changes. You are returned to the STN Setup dialog box. 

To save your changes, click Save. To test your changes before saving, or 

to use those changes for only that STN Express session, click OK. You 

will be prompted to save the configuration when you exit STN Express with 

Discover!. If you do not want to continue using these changes in 

subsequent sessions, click NO when prompted. 

Copying a setup 

To make a copy of a setup, select a setup from the Setup Names list in 

the STN Setup dialog box. Then click Duplicate. An Enter new name 

dialog box is displayed. Type a new name. Then click OK. 

The new setup is listed in the STN Setup dialog box. Select the new setup 

and click Save. Then click OK. You can modify a copied setup to 

efficiently create a new setup. 

Deleting a setup 

To delete a setup, select a setup from the Setup Names list in the STN 

Setup dialog box. Then click Delete. A STN Setup dialog box is displayed 

that asks you to confirm the deletion. Click Yes to delete the setup or No 

to cancel the request. 

If you click Yes, the setup is removed from the list displayed in the STN 

Setup dialog box. 

Password 

protecting setups 

The Password Options section in the STN Setup dialog box allows you 

to password protect access to your STN Setup dialog box. 

Click in the Password Protected check box in the Password Options 

section. Then click Set Password. The Password Protect dialog box is 

displayed. 

☞ The password is not displayed. Therefore typing it twice confirms 

that you have entered it correctly. 

Click OK. You are returned to the STN Setup dialog box. 

If the Password Protected option is enabled, you are prompted to enter 

this password when you access Setup. 

☞ Your password is required only once per STN Express with 

Discover! session.


Changing setup password 

To change an existing setup password, click the Set Password button in 

the Password Options section of STN Setup dialog box. The Password 

Protect dialog box is displayed. 

Type your current password in the Old Password text box. Then type 

your new password in the New Password text box. Reenter your new 

password in the Retype New Password text box. 

Then click OK. You are returned to the STN Setup dialog box. 

Disabling setup password 

To disable your setup password, click in the Password Protected 

check box located in the Password Options section of the STN Setup 

dialog box. The is removed. A password is no longer required when 

entering the STN Setup dialog box.

4 

Online Session on STN 

Online Session on STN 4–1 

Overview 

This chapter covers the following topics: 

• Connecting to STN 

• Capturing transcript 

• STN Online and Results window – Toolbar 

• STN Online and Results window – Status Bar 

• Using the Online menu 

• Entering commands 

• Managing transcripts while online 

• Viewing downloaded images 

• Searching STN with the Discover! wizards 

Connecting 

to STN 

1. Click Logon on the STN Express Main Menu or the Toolbar. 

2. The Select Logon Settings dialog box is displayed, if you have more 

than one setup. 

If you have only one setup created, this dialog box is not displayed. 

Select a setup name and click OK.

4–2 Online Session on STN 

Capturing 

Transcript 

The Capture Session dialog box is displayed at login. 

To capture your online session as a transcript, type a name for the 

session in the File name text box and click Open. The default type format 

is *.trn. Select another file type, e.g., RTF (Rich Text Format) if you want 

your transcript captured in Rich Text Format. 

Refer to the Appendix A. Preferences for information on how to change 

the default file type for capturing transcripts. 

Click Cancel to continue the logon process with no transcript. 

If you choose the name for an existing transcript, a message is displayed 

asking if you want to append or overwrite the existing transcript. You may 

also cancel session capture.


STN Online 

and Results 

Window 

When the connection to STN is completed, the STN arrow prompt (=>) is 

displayed in the STN Online and Results window. Online interaction with 

STN occurs in the STN Online and Results window. 

The STN Online and Results window contains: 

Content 

• the Menu bar 

• the Toolbar 

• the text area for entering commands 

• the Status Bar


Toolbar 

The Toolbar displays buttons for quick access to tools and menu options. 

You can display the name and function for a particular button. Hover the 

cursor over the button to have its function displayed in the Status Bar. 

The tool buttons include: 

Begin a new online session (Logon) 

Open transcript 

Edit transcript 

Turn off transcript capture 

Print 

Copy the selected area to the clipboard 

Paste the clipboard content to the screen 

Report Tool


Table Tool 

Predefined Report Tool 

Scroll to previous command in the session 

Scroll forward to next command in the session 

Upload structure query 

Activate the Command Window 

Run Command File 

Send break to online host 

Hyperlink all CAS Registry Numbers while connected to STN 

Send Logoff command to online host 

Force Send-Click, enter your command and press Enter 

Switch to STN Structure Drawing 

Set STN Online and Results Preferences 

View online help documents or request help by email


You may easily customize the Toolbar by removing or adding tool buttons. 

Adding tool buttons to the Toolbar 

To add a tool button, follow these steps: 

1. Right-click in the space on the toolbar where you want to add a 

button. The Toolbar Preferences dialog box appears. The option 

“Remove button or gap from toolbar” is always the initial option. Click 

Next. 

2. Click Next to view the buttons one at a time. Continue to click Next 

until you see the desired button.

3. Click OK to choose the displayed button for the toolbar. 


4. The new button is displayed on the toolbar in the slot you have 

selected. 

Removing tool buttons from the Toolbar 

To remove a tool button or a gap from the toolbar, follow these steps: 

1. Right-click on the button that you want to remove. 

2. In the Toolbar Preferences dialog box, click OK. 

The tool button that you have selected is now removed from the Toolbar.


Status Bar 

The Status Bar is located at the bottom of the STN Online and Results 

window. 

Status Bar Item 


Transcript 

File Name 

INS/OVR 

Hold On/Hold Off 

Print Off/Print On 

Online 

Running timer 

Function 

Displays a pop-up menu for the Discover! 

wizards 

Displays the directory path and the file name 

for your transcript. If you are not capturing a 

transcript, click on transcript to start capture. 

Displays the current STN file. Click this box to 

display a pop-up menu with recently entered 

files or to select From a List of files. 

Click this box to change from the insert or 

overwrite mode for entering text. 

Toggle to Hold On to stop the screen from 

continuously scrolling. Toggle to Hold Off to 

resume scrolling. 

Print On activates slave printing of information 

on the terminal window. Print Off turns off 

printing. 

Indicates an active session; the green color 

indicates ready and red indicates busy. Offline 

indicates terminated communication. 

Displays the total amount of time you have been 

connected in your online session. 

For information on how you can customize the Status Bar, refer to 

Appendix A. Preferences.


Using the 

Online Menu 

Only the non-greyed options in the Online menu are available while you 

are connected to STN.


Online menu option 

Recall Command 

Use Pagination Mode/ 

Use Continuous Scroll 

Show Text Structures/ 

Show Graphics Structures 

Suppress Screen Display/ 

Restore Screen Display 

Send Break 

Prompt Override 

Terminal Mode 

Kermit Send 

Kermit Receive 

Logoff 

Logoff Hold 

Command Window 

Function 

Recall the last command you typed online. 

You may use this command repeatedly to 

recall prior commands from the same 

session, or to edit a line to create a new 

command. Use the Up Arrow/Down Arrow 

keys as shortcuts. 

Toggle to control the scrolling of your 

online display data. Pagination Mode 

holds a screen temporarily. To continue 

displaying the next screen, click the Hold 

On box in the Status bar. 

Toggle to display text or graphics 

structures. 

Toggle to control the output display in a 

terminal window. Suppress Screen 

Display prevents STN Express from 

updating the window with new data; this 

increases the speed at which you may 

capture results. 

Send a break to interrupt a host system 

process. 

Moves your cursor to the line directly 

below the prompt and makes STN Express 

ready to accept a typed command. 

Use to change terminal emulation if you 

want to access non-STN hosts. 

Upload text or binary files using the Kermit 

protocol. 

Download a file from a host system. 

Disconnect from an online host. 

Disconnect from STN temporarily. 

Open a separate window for entering 

commands to your online host.


Entering 

Commands 

You may enter STN commands in the following ways: 

• by typing them at an arrow prompt (=>) in the text area of the STN 

Online and Results window 

• by using the Command Window 

• by using scripts 

Entering 

commands in 

the Command 

Window 

In the STN Online and Results window you can create a separate window 

for entering commands by typing them or by inserting the contents of a 

file. 

To open a Command Window, select Command Window from the Online 

menu or the tool button 

from the STN Online and Results toolbar. 

To enter commands in the Command Window: 

1. Keep this button from the right toolbar of the Command Window 

in the locked position. In the locked mode, you can type a series of 

commands and edit them. 

2. To send the commands in the Command Window to STN, use the 

buttons from the right toolbar of the Command Window: 

Button 

Function 

To send one command line at a time 

To send multiple command lines.


Inserting a command file into Command Window 

To insert the contents of another file (with commands): 

1. Click the Open button, located on the left toolbar 

2. Open a command file name in the dialog box to insert the contents of 

the command file into the Command Window. 

Saving the content of the Command Window 

Click the Save button located on the left toolbar in the Command 

Window to save the contents of the Command Window to a file. 

Clearing the content of the Command Window 

To clear the contents of the Command Window, click the Clear button 

located on the left toolbar in the Command File Window. 

Using scripts 

STN Express includes a script language that lets you automate online 

tasks. Refer to Appendix C for information about the script language. 

The Query menu in the STN Online and Results window online provides 

options for using scripts. 

Option 

Prepare Command File 

Check Command File 

Run Command File 

Function 

Create a script of commands for 

entering in your online session. Refer 

to Appendix C for information on the 

script language. 

Check a script for errors. 

Execute a previously prepared script.


Using Predefined 

Search Strategies 

STN Express provides a number of predefined search strategies that you 

can use or edit. 

To access the predefined search strategies, select Use Predefined 

Search Strategy from the Query menu. 

Managing 

Transcripts 

While Online 

While you are connected to STN, the Results menu offers the following 

options for managing transcripts in a toggle mode. 

Option 

Capture Session 

Print Session 

Start New Page 


Function 

Capture text and graphics of your 

online session to a file. 

Print the session as it occurs (slave 

mode). 

Insert a page break into the transcript 

or a slave print. 

Edit the text of an existing (already 

created) transcript file. Refer to 

Chapter 10 for information.


Viewing 

Downloaded 

Images 

Some STN files include technical drawings, chemical structures, 

trademarks, complete pages of publications, and other graphical images. 

These images are different from chemical structure diagrams in, for 

example, the Registry file because each image is downloaded into a 

separate file. Downloaded images may be in one of three file formats: 

Image Format 

TIFF 

JPEG 

GIF 

File Extension 

.tif 

.jpg 

.gif 

When you display records on STN using display formats that include 

images, STN Express automatically downloads the images to your PC. 

The files are named according to the name of your transcript, a sequential 

number, and the appropriate extension for the image type. 

For example, if your transcript is named silane.trn, the first TIFF image 

downloaded is named silane001.tif. If the next image is a GIF image, it is 

named silane002.gif. If you are not capturing a transcript, the image files 

are named IMAGE001.TIF, etc. 

When you browse a transcript offline, you have the option of viewing all 

the downloaded images in the context of your transcript. 

Viewing JPEG 

and GIF Images 

Online 

JPEG and GIF are common image file formats. Use your own image or 

graphics software to view individual JPEG and GIF images. 

QuickTime TM is provided with the STN Express 6.0 software to allow you 

to view JPEG and GIF images in transcripts, reports, and tables.


Viewing TIFF 

images online 

To view a TIFF Image while online, select View TIFF image from the File 

menu or click the View TIFF Image button from the STN Online and 

Results Toolbar. A TIFF File dialog box is displayed. 

Select a file name and click Open. The image is displayed in the TIFF 

File Display window.


View menu options 

The View menu in the TIFF File Display window provides a number of 

options for viewing the TIFF images. 

Option 

Zoom In 

Zoom Out 

Function 

Enlarge the size of the image 

Reduce the size of the image 

Rotate Change the orientation of the image, 90 

degrees, clockwise 

Flip Horizontal 

Flip Vertical 

Display the image 180 degrees 

opposite its horizontal axis 

Display the image 180 degrees 

opposite its vertical axis


File menu options 

The File menu in the TIFF File Display window contains the following 

options for displaying and printing images. 

Option 

Open 

Previous Image 

Next Image 

Print 

Print Setup 

Exit 

Function 

View the image 

View the preceding image in a series 

View the next image in a series 

Print the image. The size of the printed 

image is determined by the zoom 

setting; zoom in for a larger printed 

image, zoom out for a smaller printed 

image. 

Modify the printer setup 

Exit the TIFF File Display


Mode menu options 

You may also use the Mode menu to change the display of the images. 

Searching 

STN with 


Wizards 

STN Express with Discover! enables you to use wizards, rather than type 

commands, for some functions. Click the Discover! button 

at the bottom of the STN Online and Results window to see 

the Discover! wizards menu. 

Discover! menu


Searching 

hyperlinked data 

with Discover! 

To make it easy to retrieve data automatically, various items in STN search 

results are hyperlinked by default, such as the following: 

• CAS Registry Numbers 

• Patent numbers 

• OS (Other Source) field 

• Full-text options. 

For example, the hyperlinking of CAS Registry Numbers makes it easy to 

obtain additional data. Simply click on the hyperlinked CAS Registry 

Number. 

A pop-up menu is displayed. Select an option from the pop-up menu. 

STN Express with Discover! enters the appropriate files, conducts 

searches, and returns the requested substance data. 

STN Express with Discover! even “remembers” the last CAS Registry 

Number that you have selected. When you right-click, a pop-up menu 

displays again, showing you the previously selected CAS Registry 

Number. 

ANALYZE wizard 

While you are connected to STN, you may also use the ANALYZE wizard 

to display the analyzed fields from search results as a histogram. Follow 

these steps. 

1. Click the Discover! button. Select Analyze Answers from the 

Discover! menu.


2. The ANALYZE wizard is invoked. Click Next. 

3. Highlight the answer set for analyzing. Click Next.


4. Select the field to analyze. Click Analyze. 

5. Select the range of terms to analyze. Click Display.


6. The analyzed results are displayed as a histogram. 

To display the answers from the histogram, click on one of the boxes 

on the left and click the Display these answers button. 

To print the histogram, click the Print button. 

To save the histogram, click Save As. 

7. If you click Save As, the Select Analyze Results File dialog box is 

displayed. Enter the name for the saved file and select the format, 

e.g., Excel Files.


8. The saved results are displayed as a bar graph in Microsoft Excel.

5 

Using non-STN Hosts 

Using non-STN Hosts 5–1 

Overview 

In addition to STN, STN Express with Discover! provides automatic logon 

and other features for the following “supported” online hosts: 

DIMDI 

Datastar 

Dialog 

EINS 

NLM 

Ovid 

Questel·Orbit 

STN Express also lets you define host settings for other, “unsupported” 

online hosts so that automatic features will function. In addition, manual 

emulation, with no automatic features, can be used to connect to any 

computer or online host. 

This chapter covers the following topics: 

· Logon setups for supported non-STN hosts 

· Logon setups for other hosts 

· Online session on non-STN hosts 

Refer to Chapter 3 for information about logon setups for STN and general 

information about managing setups. Refer to Chapter 4 for information on 

online session on STN.

5–2 Using non-STN Hosts 

Logon Setup 

for Supported 

non-STN 

Hosts 

To create a new logon setup for a supported host, click the Setup 

button on the STN Express Toolbar or click the Setup menu and select 

Connections. The STN Setup dialog box opens. Click New to open the 

Setup Definition dialog box. 

Creating a logon 

setup 

Basic logon 

setup values 

Setup Name 

The Setup Name identifies a specific setup. The name must be 20 

characters or fewer and can include any combination of letters, numbers, 

special characters, and spaces. Suggested setup names help identify the 

host (Questel, in this example) and communication path (COM1), e.g., 

Questel via modem. 

Host Name 

The Host Name identifies the online host that you want to access in this 

setup. 

Login ID 

Enter your login ID for the online host you selected in the Login ID text 

box. Entering a login ID at this time is optional. If you do not enter it here, 

you will be prompted to enter it when you log on to the host 

Password 

Enter your host password in the Password box. For security, an asterisk is 

displayed for each password character you type. Your password is stored 

in the express.ini file in an encrypted form. Entering a password at this 

time is optional. If you do not enter it here, you will be prompted to enter 

when you log on to the host. 

Path Tabs 

Select Path 1 to define the communication path to reach the online host 

you selected. Select Paths 2-4, as needed, to define alternate 

communication paths to the online host. When STN Express tries to


connect to the host, it first uses Path 1. If Path 1 fails to connect, STN 

Express tries the next path until the connection is made or there are no 

more paths to try. 

+ Only Path 1 is available when the Host Name is set to Manual 

Emulation. 

The Host Settings tab, to the right of the Path tabs, contains settings that 

are specific to the selected online host. Usually these settings do not need 

to be changed. Refer to the Host Settings section later in this chapter for 

details. 

Connect via 

Select a communication method from the Connect via pulldown menu to 

connect to the online host you selected. 

The method that you choose controls the information that is required in 

the Communication Settings section. This is described further in the 

Advanced Communications Settings section, later in this chapter. 

Connect via options are: 

· Winsock (Internet) - select if your network software supports 

Windows Sockets and Telnet from your PC (most do). When 

selected, the Host Name or IP Address, Port, and Echo fields are 

displayed. Overwrite the host name or host address, if different 

from the default (rare). Set Echo to No if you do not want STN 

Express with Discover! to echo characters as they are typed. The 

Port setting of 23 (Standard Telnet) in most cases should not be 

changed. 

· Dial-Up Networking - STN Express with Discover! lists all 

connections defined in Windows Dial-Up Networking. Dial-Up 

Networking connections are most commonly used to define 

connections to the Internet via an Internet Service Provider (ISP). 

STN Express with Discover! will then attempt to use the Standard 

Windows interface to Dial-Up Networking (in WININET.DLL) when 

a logon is attempted. You will be prompted to connect to your ISP 

as needed. NOTE: Winsock is the underlying connection type for 

this option. 

· Modem - STN Express with Discover! lists all modems installed in 

the Windows Modems Control Panel. This option eliminates the 

need to set many of the modem options, because this information 

is obtained directly from Windows. Most users will only need to 

specify a phone number for this option. NOTE: If you cannot 

make a connection using this method, try using a COM Port 

option. 

· COM1, COM2, COM3, or COM4 - select to connect via a serial 

port, e.g., to a modem, terminal server, host system.


Standard Logon 

and Logoff 

methods 

The logon method includes connecting to the online host and logging on to 

the host. Use a Standard Logon Method to connect to a supported host 

system via one of the supported networks. Use a Custom Logon Method 

when you connect via an unsupported network and when you log on to an 

unsupported host. A custom logon method is also needed for certain 

combinations of supported networks, such as when a network modem pool 

is reachable by a Winsock connection. See Custom Logon and Logoff 

later in this chapter for details. 

Standard Logon 

To use a standard logon procedure, click the radio button next to 

Standard in the Logon Method section and select one of the supported 

networks from the pulldown menu. STN Express with Discover! 

automatically inserts the scripts necessary to connect to the network and 

the host you selected, and also inserts the values that the scripts require. 

Modify these values, as needed. 

For example, if a setup is defined to connect to DIMDI host via Tymnet, 

using a tone or pulse modem, STN Express with Discover! selects several 

scripts from the Scripts folder including the following: 

· a script that sends dial commands to a modem 

· a script that connects to DIMDI via the Tymnet 

telecommunications network 

· a script that logs on to DIMDI 

+ If you are connecting via a gateway or firewall that requires a 

separate logon, see Settings for Winsock (Internet) Setup for 

Supported non-STN Hosts later in this chapter and Appendix F. 

Standard Logoff 

Click the radio button next to Standard in the Setup Definition dialog box 

to tell STN Express with Discover! to use the “discnct” script to disconnect 

the communication path. This script handles most connections, including 

those made through a modem and via Winsock. If STN Express with 

Discover! does not correctly disconnect the communication path, you will 

need to define a custom logoff. See Custom Logon and Logoff later in 

this chapter for more information.


Network Logon 

The Network Logon section in the Setup Definition dialog box is displayed 

when STN Express with Discover! recognizes that the Host Name and 

Connect via combination you selected require information to make the 

network connection. You may need to enter any of the following values: 

· NUA (Network User Address) - the address of the host on the 

network you selected. The value may be a character string, e.g., 

stnc, or a numerical string, e.g., 03106001467 

· NUI (Network User Identifier) - a character string that identifies 

the user to the network. Some networks require this. 

· NUP (Network User Password) - a password to confirm the 

identity of the user on the network. Some networks require this. 

To keep the NUP entry secure, only asterisks are displayed when you 

type this value. It is stored in the express.ini file in encrypted form. To 

confirm your NUP, you are prompted to re-enter the password after you 

select OK from the Setup Definition dialog box. 

STN Express with Discover! provides default NUA values for a limited 

number of combinations of hosts and networks. If a default value is not 

available for the combination you have selected, an error message is 

displayed when you try to use the setup. If this occurs, return to the Setup 

Definition dialog box. Then select the path that failed and fill in the NUA 

field. 

Settings for 

Winsock 

(Internet) setup 

for supported 

non-STN hosts 

When Connect via is Winsock or a Dial-up Networking item, settings 

specfic to Internet TCP/IP connections are available. The settings are 

· Host Name or IP Address - the name or address of the host 

computer to which STN Express will connect. For example 

dialog.com or 192.132.3.254. These values are provided 

automatically for supported online hosts. 

If you must connect to the host through a telnet gateway, enter the 

name or IP address of the gateway and see Appendix F for more 

information. 

· Port - the TCP/IP port number for telnet (Winsock) connections. 

The default is 23, and you should change this only if your 

organization has a firewall that uses a different port for the telnet 

protocol. 




type, try changing the Echo selection.


Modem settings 

for supported 

non-STN hosts 

When a modem or COM port is selected in the Connect via list, the 

Communications Settings section of the Setup Definition dialog box 

contains modem communication parameters. 

The following settings are available: 








If the online host does not recognize the Break signal, you may 

need to increase this value. If the Break command disconnects 

you from your network, you may need to decrease this value. 




telephone. 

· Primary Phone # - the telephone number for the network provider 

you selected. 

· Secondary Phone # - an alternate telephone number for the 

network provider, used if the primary phone number fails to 

connect. 

Use the Windows Modems Control panel to change other communication 

settings.


Connect via COM 

port settings 

The following settings are available: 

· Echo - specifies whether to echo characters as they are typed. If 

you cannot see the characters you are typing or if you see two 

characters for every one that you type, try changing the Echo 

selection. 




If the online host does not recognize the Break signal, you may 

need to increase this value. If the Break command disconnects 

you from your network, you may need to decrease this value 

· Speed (bps) - the serial port speed used to connect to your 

modem. The speed may range from 300 to 57600 bits per 

second. If your modem’s maximum speed is not listed, select next 

higher speed. 

· Flow Control – the method of synchronizing communications 

between the PC, modem, and online host. Flow Control is used to 

prevent the overflow and loss of data from an online host. 

Hardware is the default and should be used in most cases. Data 

loss may occur if this setting is not synchronized with your 

modem’s settings. 

· Data bits, Stop bits, and Parity - data transfer settings. Data 

bits 8, Stop bits 1.0, and Parity NONE are nearly always the best 

choices and are the defaults. Use 7, 1.0, and EVEN when the 

maximum modem speed is lower than 9600 baud.





telephone. 

· Primary Phone # - the primary telephone number for the network 

provider 

· Secondary Phone # - an alternate telephone number for the 

network provider. 

Advanced 

Communication 

Settings 

The Advanced option in the Communications Settings section of the Setup 

Definition dialog box is used to provide information used by three distinct 

features of STN Express with Discover!. They are: 

· Connecting to an online host through a telnet gateway, firewall, or 

proxy server. Refer to Appendix F for details. 

· Sending an initialization string to a modem 

· Sending a character string instead of a standard Break command 

Advanced 

dialog box 

Click the Advanced button to open the Advanced dialog box. 

Enter the appropriate information. Click OK when all specifications are 

entered. Or click Cancel to cancel all changes.


Advanced dialog 

box values 

Modem Configuration 

Enter values in the Modem Configuration section to define an 

Initialization String for the modem. If you specify a value in this field, the 

string is sent to the modem before the dial command is issued, and a 

response of OK is expected. See your modem manual for details about 

modem commands and options. NOTE: Not recommended if you have 

selected the name of your modem from the Connect via list. 

The Phone # box in the Modem Configuration section normally displays 

the value of the Primary Phone # for this path. For the special case when 

the phone number fields in the Communication Settings area are not 

available, e.g., for Winsock connections to a network modem pool, use 

this field to specify a telephone number. 

Other 

Enter the appropriate value in the Break sequence text box to define a 

character string that you want STN Express with Discover! to use as a 

break indication to an online host. This value is needed only for systems 

that do not support a standard break. 

Host Settings 

Select the Host Settings tab to see settings that are specific to the 

selected online host. Some of the settings enable features such as 

automatic logon to the host. 

+ Fields in the Host Settings tab are unique to the host that you 

select. 

+ The Host Settings tab is not available when you select Manual 

Emulation from the Host Name pulldown menu. 

Host Prompts 

The Host Prompts window may list up to five prompts issued by the host 

you select. STN Express with Discover! uses this information to determine 

when the host is ready to receive the next command. This supports several 

STN Express with Discover! features, such as the Command Window and 

command line recall while you are logged on. 

STN Express with Discover! provides default values in the fields for the 

online hosts in the Host Name list. For STN hosts, these default values 

cannot be changed. For other hosts, these default values can be changed, 

although caution is advised.


When searching for a host prompt, STN Express with Discover! looks for 

an exact match with one of these strings, including blanks and control 

characters. The search begins with the last character received from the 

host and works backward for the length of the string. The following 

conventions are used to represent special characters in these strings: 

# - any string of digits, e.g., “102”, or the “#” character 

- Blank (represented by a space) 

[M - Carriage return 

[Q - Control Q (XON) character 

[J - Line feed 

[[ - One left square bracket (“[“) 

Logoff Messages 

The Logoff Messages window lists up to five text strings that are issued by 

the host at logoff. STN Express with Discover! uses this information to 

determine when the session with the host has ended. When this happens, 

the processing defined in the Logoff Method section of the Setup 

Definition dialog box is executed and your connection is closed. 

STN Express with Discover! provides default values in the Logoff 

Messages window for the host listed in the Host Name field. For STN 

hosts, these default values cannot be changed. For other hosts, these 

default values can be changed, although caution is advised. 

STN Express with Discover! looks for an exact match with one of the 

Logoff Messages strings to any of the data received from the host. This 

match includes looking for any trailing blanks. Matching of control 

characters is not supported. 

Command 

Window 

Click a Ö in the Command Window box to enable STN Express with 

Discover! to open a Command Window when you log on to a host. The 

Command Window can also be turned off and on while logged on to an 

online host. 

Click a Ö in the Close Window at logoff box to tell STN Express with 

Discover! to close the session window after you log off the host. If you 

prefer to scroll back through your session or capture a transcript after you 

log off, do not select this option. 

Highlight ON 

Sequence 

Enter a character string in the Highlight ON Sequence text box to tell STN 

Express with Discover! how the host system will indicate hit term 

highlighting during an online session and when browsing a transcript. The 

string you enter must be unique as highlighting is indicated at any point 

where this term appears. Matching of control characters is not currently 

supported.


Highlight OFF 

Sequence 

Enter a character string in the Highlight OFF Sequence text box to tell STN 

Express with Discover! how the host system will indicate the end of a 

highlighted term. Matching of control characters is not currently 

supported. 

Execute at first 

Host Prompt 

window 

Up to five commands may be entered in the Execute at first Host Prompt 

window. The first command is sent when the first host prompt is received, 

and the remaining commands are sent, one at a time, with each 

succeeding the host prompt. 

By default, a carriage return is sent after each line. The keyword NOCR 

may be added as the last word on the last line that you enter to indicate 

that this line is to be displayed in the STN Online and Results window, but 

not sent. This allows you to enter data after the defined character string, 

before it is sent. 

Choice of Service 

and Language 

options 

The Choice of Service and Language options are displayed only if you 

have selected Questel from the Host Name pulldown menu. The Choice of 

Service value should be from 1 to 6 characters in length and is sent at the 

first Questel prompt. The language you enter is the language in which you 

want to interact with Questel. 

+ For the Markush DARC service, the language is not set automatically 

at logon because of the time required to do this. However, the script 

Qst_op.sc, located in the Scripts folder, can be run after logging on to 

set the language and other options used by this service. If you access 

this feature frequently, copy the Qst_op.sc script to the User Scripts 

folder to access it more easily. See Appendix C, for instructions on 

running an STN Express with Discover! script. 

Logon Setups 

for Other 

Hosts 

To create a setup for a host that is not currently supported by STN 

Express with Discover!, either select Manual Emulation or Other from 

the Host Name pulldown menu in the Setup Definition dialog box. 

Select the Manual Emulation host name to create a setup that does not 

use any of the automatic features, e.g., automatic logon, host prompt 

recognition, special handling of host highlighting characters, of STN 

Express with Discover!. When selected, STN Express with Discover! 

requires only values in the Communications Settings section of the STN 

Setup dialog box.


Manual Emulation 

Use the Manual Emulation mode to bypass the automatic features of STN 

Express with Discover!. In this case, STN Express with Discover! only 

allows for terminal emulation, without automatic dialing, automatic logon, 

etc. 

To create a Manual Emulation setup: 

1. Type a name in the Setup Name text box 

2. Select Manual Emulation from the Host Name pulldown menu 

3. Select the appropriate connection method from the Connect via 

pulldown menu 

4. Modify the values for the Communications Settings if necessary 

5. Click OK. 

Other as host 

name 

Select the host name Other to create a setup for a host that is not in the 

Host Name list. A Custom Logon Method is required. You may click the 

Host Settings tab to define the host prompts, logoff messages, and 

highlight characters. 

Use the Other mode to create a setup that supports some of the automatic 

features of STN Express with Discover!. However, you must provide a 

script for logging on to the host, and you must provide the values needed 

in the Host Settings tab of the Setup Definition dialog box. 

To create a setup for another host: 

1. Type a name in the Setup Name text box 

2. Select Other from the Host Name pulldown menu 

3. Click the radio button next to Custom in the Logon Method section. 

Then click Configure. 

4. Click the Watch Me button to create a script for logging on the host 

system. Then click OK. 

5. Click the Host Settings tab and fill in the Host Prompts fields 

If you leave the Host Prompts fields blank, you will be able to interact 

with the host, but features such as the Command Window will not 

work. 

6. Optionally, fill in the values in the Logoff Messages field on the Host 

Settings tab 

If you do not add a message to the Logoff Messages fields, STN 

Express with Discover! may not disconnect the session after logoff. 

You can disconnect the session manually by selecting Drop DTR 

from the Online menu or by closing the window that contains the 

online session. 

7. Optionally, fill in the values in the Highlight ON Sequence and 

Highlight OFF Sequence text fields 

8. Click OK.


Custom 

Logon and 

Logoff 

Use custom logon and logoff methods when STN Express does not support 

the telecommunications network or online host you choose. If you write 

your own logon or logoff scripts, review the Predefined Setup Variables 

section in Appendix C. Script Language. 

A custom logon requires you to select scripts to tell STN Express with 

Discover! how to connect to your network and host. Scripts typically are 

used to execute a step in the logon process. For example, one script might 

have the modem dial a telephone number and connect to a network; a 

second script may connect through the network; a third script may log on 

to the host. 

Custom Logon 

To create a custom logon procedure, click the radio button next to 

Custom in the Logon Method section. Then click the Configure button. 

The Custom Logon dialog box is displayed. The Scripts Folder box 

displays a list of scripts from either the User or Standard Scripts folder. 

The Standard scripts folder corresponds to the Predefined Scripts folder 

in General Preferences. The User scripts folder corresponds to the User 

Scripts folder in General Preferences. 

The Selected script list box displays the scripts that have been selected 

for this custom logon setup. The scripts will be executed in the order 

shown as part of the connect and logon process. To change the order of 

the scripts in the Selected script list, select a script and click the up (s) 

or down (t) arrow to move the script name one position at a time. 

To add a script to the logon procedure, select (highlight) a script in the 

Scripts Folder list. Then click the Copy>> button to copy the script to the 

Selected script list. Click the Watch Me button to insert the watchme.sc 

script into the Selected script list window. The watchme.sc script can be 

used more than once in the Selected script list. For more information, 

refer to the Watch Me section later in this chapter. 

Click the Delete button to delete a script from the Selected script list. 

Click the View button to display the actual script for a script name that you 

select from the Scripts Folder window. 

Click OK to when you have completed your entries to the Selected script 

list window and to return to the Setup Definition dialog box. The scripts 

you selected are displayed in the Custom Logon Script List box.


Custom Logoff 

Use a custom logoff procedure when the method to disconnect from an 

online host is not successful or is not supported by the standard logoff 

method. 

The Logoff Method section in the Setup Definition dialog box defines 

how STN Express with Discover! will disconnect the communications path 

when you log off from an online host. 

When you log off, STN Express with Discover! scans the output from the 

host system looking for the logoff messages defined under the Host 

Settings tab in the Setup Definition dialog box. When it locates a 

message, STN Express with Discover! knows that is has logged off of the 

remote system. It then disconnects the communication path using the 

method defined in this section. 

+ If the communication path is not disconnected correctly, you may get 

a “Communication Port In Use” error when you try to use a program 

that requires the use of a communication port. 

The steps for defining a custom logoff are nearly identical to that for 

defining a custom logon. Refer to Custom Logon in this chapter for 

details. 

Online 

Session on 

non-STN 

Hosts 

The STN Express with Discover! STN Online and Results menus vary with 

the online host that is used. Because STN Express with Discover! is 

specifically designed for STN, more online features and commands are 

available when connecting to STN. Basic features, such as capturing a 

transcript and sending a break to interrupt the host, are available for any 

online host. 

The File and Edit menus function the same for all online services. 

The Online and Terminal menus provide similar commands for controlling 

your online or terminal session. 

The Query menu provides commands to take advantage of special 

features while online to STN or Questel. These include uploading structure 

queries, running command files (including WPI strategies), and using 

predefined search strategies. 

The Results menu is used to capture items displayed in the terminal 

window to a file. Use these files to browse, print, edit, or export.


Terminal menu 

The Terminal menu is available if you are connected to a vendor other 

than the seven non-STN hosts supported by STN Express with Discover! 

and when you are logged on through manual emulation.


Terminal menu 

options 

Option 

Use Pagination Mode 

Use Continuous Scroll Mode 

Suppress Screen Display 

Send Break (Ctrl+B) 

Prompt Override (Ctrl+Enter) 

Terminal Mode 

VT320 Settings 

VT320 Keyboard 

Setup Terminal Parameters 

Result 

Pause after displaying a window full of 

information. Click Hold On in the status 

bar to display the next page. 

Display information from the online host 

continuously, without pausing. 

Stop the display of information in the 

STN Online and Results window. Even 

when transcript capture is on, no 

information is saved in the transcript file 

when Suppress Screen Display is 

selected. 

Send a break signal to the online host to 

interrupt a command or another function 

If STN Express does not recognize a 

host prompt, it will not let you type a 

command. Use Prompt Override to let 

you type. 

Specify the terminal emulation mode. 

See Terminal Mode later in this chapter 

for more information. 

Specify terminal settings when using 

VT320 terminal emulation. See VT320 

Settings later in this chapter for details. 

Specify the keyboard configuration when 

using VT320 terminal emulation. See 

VT320 Keyboard later in this chapter for 

details. 

Select communications settings for 

certain types of modem connections. 

Refer to the Setup Terminal Parameters 

section later in this chapter for more 

information.

Terminal menu 

options 

(continued) 

Option 

Kermit Send 

Kermit Receive 

Logoff 

Execute Script 

Watch Me 

Drop DTR 

Raise DTR 


Result 


Upload a file to an online host. STN 

Express can send text or binary files. 

Kermit protocol is used with the timeout 

interval of 10 and the packet size of 94. 

Download a text or binary file from the 

online host. A packet size of 4000 is 

recommended. 

This option is not available for Manual 

Emulation or for setups defined using the 

Other host name. 

Run a script written in the STN Express 

script language. For information, refer to 

Appendix C, Script Language. 

STN Express with Discover! records all 

activities from your online session into a 

script file. The Watch Me menu item is 

a toggle switch. 

Set the modem’s Data Terminal Ready 

circuit to OFF. 

Set the modem’s Data Terminal Ready 

signal to ON. 

Open a box at the bottom of your online 

window that can be used to type 

commands and other functions. The 

Command Window is available for all 

hosts, but you must define the host 

prompts in the logon setup (Host 

Settings tab) for all features of the 

command window to work properly.


Terminal Mode 

Options 

Three terminal emulation modes are available: 

· TTY 

· Tek41xx 

· VT320 

The Terminal Emulation modes interpret escape sequences in the data 

stream. These direct the receiving terminal either to perform a particular 

operation or to interpret characters. An escape sequence is one or more 

characters that are transmitted to define a specific control function. When 

STN Express with Discover! receives characters from a remote host, the 

selected terminal mode interprets them accordingly. 

+ The Hold On/Hold Off and Capture commands function in all three 

emulation modes. 

TTY mode 

TTY is the default terminal mode. It supports a number of STN-specific 

escape sequences.


Tek41xx mode 

STN Express with Discover! supports the basic Tektronix 4100 sequences. 

The graphics operations are supported with line vectors and text. 

Advanced graphics features such as Graphtext rotation, pixel copying, 

rectangle filling, and others are not supported. 

The Tek41xx emulation is based on a 1024 by 768 coordinate system. If 

this exceeds the screen dimensions of your display, you may lose some 

definition when mapping the coordinate system. Maximizing the STN 

Online and Results window is advised. 

Although standard Tek4100 escape sequences for printing are not 

supported by STN Express with Discover!, you may capture the data to a 

transcript file to print later. If the current transcript file is SESSION.TRN, 

the TEK data are captured to the file SESSION.TEK. This file may be 

browsed or printed in the normal manner. 

Three basic modes support this emulation. Switching between these 

modes is performed transparently and automatically by escape sequences 

that are sent by the host. 

1. Alpha Mode - When your terminal is in the Alpha Mode, it 

interprets received characters and displays ASCII characters. 

When the cursor reaches the bottom of the display screen, the 

display scrolls to allow you to view the incoming data. 

2. Vector Mode - When your terminal is in the Vector Mode, the 

incoming characters are interpreted as a series of XY coordinate 

positions. The emulator moves the current graphics position to the 

first XY position and draws lines (vectors) to any subsequent 

positions. Graphics are displayed at the XY positions. 

3. GIN Mode - When your emulator receives the ENABLE 4010 GIN 

command from its host, it displays a cross-hair cursor. Position 

the cursor at the required location and then press a key or click 

your mouse button. The emulator sends a 4010 GIN REPORT. 

This escape sequence contains details of the key pressed and the 

current cursor position. 

It is typical for the host to have previously entered the Vector Mode to 

draw the input screen with text. Options are displayed at set locations on 

the screen. The host application can map the GIN REPORT key/ 

coordinate combination to carry out specific actions.


VT320 mode 

STN Express with Discover! supports limited DEC VT320 terminal 

functions. It supports basic 80 or 132 column mode with 24 lines. It does 

not support printing, selective erase, soft character sets, user-defined 

keys, or the 25th status line. The cursor position (line and column) is 

displayed on the STN Online and Results status bar. 

Although printing is using VT320 escape sequences is not supported, 

standard STN Express with Discover! print features are available. Save 

your data to a transcript and print the transcript file or use the Print 

Selected option on the File menu while online. 

When you are in the VT320 Mode, VT320 Settings and the VT320 

Keyboard options are enabled in the Terminal menu. 

VT320 Settings 

Select VT320 Settings from the Terminal menu to change specific 

display options. The Terminal Settings dialog box is displayed. 

· Number of Columns - sets the terminal width to either 80 or 132 

columns. The default is 80. Some VT320 applications can operate 

in either 80 or 132 column mode. 

· Terminal Modes - includes the following terminal options: 

Line Wrap - if selected, received characters are 

automatically wrapped onto the next line. If not selected, 

characters received after the last allowable character on a 

line overwrite existing characters. 

Local Echo - if selected, keyboard characters are displayed 

on the screen and sent to the host. The host does not need to 

echo the characters. If not selected, the host is responsible 

for sending the characters back to the terminal for display. 

Auto-repeat - if selected, you may hold a key and that key is 

sent repeatedly to the host. If not selected, only one character 

is sent to the host each time a key is pressed.


· Backspace - determines which character to send the host when 

the backspace key is pressed. Select BS to send a backspace 

character (8) to the host. Or, select DEL to send a delete 

character (127) to the host. 

· End of line - determines which character to send the host when 

the carriage return key is pressed. CR sends only a carriage 

return character, and CR/L sends a carriage return followed by a 

linefeed. 

· Control - select 8bit to obtain faster control sequences. The data 

path to the host must recognize 8-bit characters. If problems 

occur, select 7bit. All hosts recognize 7-bit characters. 

After you change one or more options, click OK to save and use the 

settings. 

VT320 Keyboard 

Select VT320 Keyboard to change keyboard options. The Keyboard 

dialog box is displayed. 

· Keypad - determines which character to send the host when a 

key on the numeric keypad is pressed. Select Numeric to 

transmit the actual character you press, i.e., number, comma, 

plus sign. Select Application to transmit a standard sequence of 

characters to the host. These characters are not user-definable. 

· Cursor Keys - select Normal to send standard ANSI cursor 

sequences. Select Application to send an application sequence 

of characters to the host. 

· Cursor - select Blanked to hide the cursor. Select Visible to 

show the cursor. 

· Cursor Type - select Block or Underline cursor style. 

After you change one or more options, click OK to save and use them.


Setup Terminal 

Parameters 

Setup Terminal Parameters is active only when the logon setup Host 

Name is Manual or Other and a COM port is selected in Connect via. A 

Communications Settings for Terminal Emulation dialog box is 

displayed. 

Change the settings to meet your communication needs. When you have 

modified your communications settings, click OK to save and use the 

settings.

Structure Queries 6–1 

6 

Structure Queries 

Structure queries may be built in the STN Express with Discover! 

Structure Drawing program. Structures may be drawn as Standard, 

Specinfo, WPI, and Questel structure types. 

The basic structure-building techniques are discussed in this chapter and 

are applicable to all structure types, including reaction queries. 

Chemical structures may be built offline. This is the best economic 

approach as no connect time or online costs are incurred as you 

construct the query. Simply draw the structure. Then during an online 

session, upload the query by selecting Upload Structure Query from the 

Query menu. 

For extensive documentation and training on structure searching 

strategies, contact your Customer Service representative. 

Launching 

Structure 

Drawing 

Select Prepare Structure Query from the Query menu or click the 

Prepare Query button on your Toolbar. The Structure Drawing program 

opens, along with a new Untitled “Standard” window.

6–2 Structure Queries 

The Structure Drawing window includes its own Structure Drawing menu 

bar. These menus contain the commands and subcommands to access 

structure drawing tools. It also contains toolbars and a tool palette that 

give quick access to drawing tools, atoms, and bonds. 

Atoms & 

Bonds 

Toolbar 

The Atoms & Bonds Toolbar provides quick and easy access to common 

atoms and bonds. If atoms or bonds that you need are not located here, 

access the Draw menu in Structure Drawing. 

☞ The term “atom” is frequently used in this User Guide to refer to 

atoms, variables, shortcuts, G-groups, and the points of attachment 

for G-group fragments. 

Current 

Atom Box 

Common Atoms 

Current 

Bond Box 

Common 

Bonds 

Reset 

Atom/Bond 

The Current 

Atom Box 

The Current Atom box displays the symbol of the current atom that is 

being used. This symbol is inserted into the ring or chain that you draw. 

The default atom is C, carbon. 

Right-click in the Current Atom box to display the Atom Selection dialog 

box. 

Type a new atom in the Symbol text box or use the scroll bar to locate the 

atom you need.


Then click Single Use to insert the selected atom one time. Click Multiple 

Use to insert the atom more than once and retain it as your default. Click 

a ✓ in the Exclude box to exclude the selected atom from retrieved 

substances during an online search. Click Cancel to cancel the Atom 

Selection request. 

You may also left-click in the Current Atom box to display either the 

Periodic Table dialog box, the Atom Selection dialog box, or the List 

dialog box. These dialog boxes are used to select atoms for single or 

multiple use in a structure drawing. The dialog box that displays depends 

on the selection in the Drawing section of your Structure Drawing 

Preferences. Refer to The Preferences! Menu section, later in this 

chapter, for more details. 

The Common 

Atoms 

The Common Atoms are icons for those atoms that are most frequently 

used in structure drawing. 

Single-click an atom icon to insert it into a structure once. After you insert 

the atom, the previous default atom is reset in the Current Atom box. 

Double-click an atom icon to insert it into a structure more than once and 

to retain it as your atom default. 

You may customize the Common Atoms to include the atoms you most 

commonly use. To do so, right-click on an atom that you want to replace. 

The Atom Selection dialog box is displayed. Locate and click the atom 

you want to insert on the palette. Then click OK. The atom you selected 

permanently replaces the atom that was previously in that position. 

The Current 

Bond Box 

The Current Bond Box displays the bonds that you are currently inserting 

into your structure. To select another bond, click in the Current Bond 

box. The Bond Selection dialog box is displayed. 

The radio button of the current bond is selected. To choose a different 

bond, click the radio button next to that bond.


Then click Multiple Use to insert the bond more than once and to retain it 

as your default selection. Click Single Use to insert the bond once. After 

you insert the bond, the previous default bond is reset in the Current 

Bond box. Or click Cancel to cancel the request. 

The Common 

Bonds 

The Common Bonds are the bonds you most often used in structure 

drawing. If a common bond is your current default, it is highlighted and is 

also displayed in your Current Bond box. By default, the single bond and 

the double bond appear in the palette. 

Single-click the Single bond or the Double bond to insert it into your 

structure once. After you insert the bond, the previous default bond is 

reset in the Current Bond box. Or double -click the Single bond or 

Double bond to insert it into your structure more than once and to retain 

it as your default bond. 

Click on the Current Bond box to display the Bond Selection dialog box. 

Select a different bond by clicking the appropriate radio button. Click 

Multiple Use or Single Use. Refer to the previous section for more 

details. 

To customize one of the common bonds, right-click on either existing 

common bond. The Bond Selection dialog box is displayed. Select a 

bond and click OK. The bond you select becomes a common bond. 

Reset Atom/Bond 

Defaults 

Click the Reset Atom/Bond button to quickly return to the STN Express 

with Discover! Structure Drawing atom and bond defaults. The atom 

default is C, carbon, and the bond default is a single bond. 

☞ You may also press the Spacebar to reset the atom/bond defaults. 

Toolbar 

(Function 

Keys & Menu 

Shortcuts) 

The Toolbar provides quick and easy access to common file functions and 

to menu shortcuts. These tools are also located in various menus within 

Structure Drawing.


Customizing the 

Toolbar 

You may customize this toolbar by right-clicking on any button shown or in 

a vacant button position. This displays the Structure Drawing Toolbar 

Preferences dialog box. 

A tool button is displayed along with a description of its function in the 

Description section of the dialog box. 

If you right-click on a specific button or a specific vacancy (toolbar gap), 

click OK to replace the button or gap. Or, click Next to display the next 

button. When you locate a button you want to insert in the button position 

that you clicked, click OK. Or, click Cancel to cancel this request. 

You may also click Previous to backtrack to a button you already viewed. 

You may also customize the position of the Toolbar by left-clicking a gap 

on the tool bar. A selection box is displayed. 

Drag your cursor over a selection to highlight it. Then click to select that 

option. The positions include: 

• Vertical/Horizontal - select to display the Toolbar horizontally, 

above the Structure Drawing window 

• Double Line/Single Line - select to display the Toolbar in a single 

line or a double line 

• Close - select to close the Toolbar 

☞ If you close the Toolbar, you must access the Layout tab of 

Structure Drawing Preferences and then click Visible in the Toolbar 

section to display it. 

☞ You may also customize Toolbar positioning in the Layout option of 

Structure Drawing Preferences.


List of Toolbar 

Buttons 

Toolbar Button 

Description 

Open a new Standard STN structure drawing window 

Open a new SpecInfo STN structure drawing window 

Open a new WPI STN structure drawing window 

Open a new Questel structure drawing window 

Save the current structure 

Save the current structure with a new name 

Open existing structure drawing queries 

Display the carbon atoms as C, dots, or angles 

Toggle the Query Attribute pop-up display, i.e., point your cursor on 

any item in a query and its attributes are described 

Print the current structure query 

Set Structure Drawing Preferences 

Verify the query’s attributes 

Cut the selected structure or structure fragment and place it on the 

clipboard 

Copy the selected structure or structure fragment and place it on the 

clipboard 

Paste the clipboard contents into the current structure query 

Fuse two structures or structure fragments together 

Undo the last action 

Center the structure in the Structure Drawing window


Toolbar Button 

Description 

Display the Shortcut menu, which contains shortcuts to insert one or 

more times in your query 

Display the Variable Selection menu, which contains a variable to 

insert one or more times in your query 

Toggle the use of the reaction drawing mode 

Toggle the use of the Functional Group drawing mode 

Show Structure Drawing Help 

Analyze the structure query and suggest filters 

View existing filters 

Return to original application 

Fast return to main program 

View the existing Functional Group command file 

Switch to STN Terminal Emulation mode and logon to an online 

vendor


Tool Palette 

The Tool Palette provides the tools used to create or modify structure 

queries. 

☞ The Reaction and the Functional Group drawing tools are located on 

the Tool Palette and are activated when you click the RXN button or 

the FG button on the Toolbar. 

Pencil Tool 

Ring Tool 

Chain Tool 

Eraser Tool 

Selection Tool 

Lasso Tool 

Text Tool 

Reaction Arrow Tool 

Reaction Role Tool 

Reaction Site Tool 

Atom Mapping Tool 

Functional Group Tool 

OR Tool for Functional 

Groups 

- draw atoms/bonds using the current atom/bond 

- draw 3 - 15 member ring systems 

- draw 1 - 30 member chains 

- delete objects in the structure query 

- select (highlight) objects in the structure query 

- select (grab) objects in the structure to move 

- add text to your screen (not searched) 

- set up a chemical reaction between structures 

- specify the roles of the participants in a reaction 

- specify which bonds change in a reaction 

- specify correspondence between atoms in reactant and product 

- add functional groups in a query for CASREACT on STN 

- link functional groups with an OR operator 

Customizing the 

Tool Palette 

You may customize the position of the Tool Palette by left-clicking the open 

position in the tool palette. A small selection box is displayed. 

Drag your cursor over a selection to highlight it. Then click to select that 

option. The positions include: 

• Horizontal/Vertical - select to display the Tool Palette 

horizontally, above the Structure Drawing window 

• Double Line/Single Line - select to display the Tool Palette in a 

single line or a double line 

• Close - select to close the Tool Palette 

☞ If you close the Tool Palette, you must access the Layout option of 

Structure Drawing Preferences and then click Visible from the 

Palette section to display it. 

☞ You may also customize Tool Palette positioning in the Layout option 

of Structure Drawing Preferences.


Pencil Tool 

The Pencil tool is used to place or change atoms or bonds. Click the 

Pencil tool to activate the pencil to draw atoms and bonds with the current 

atom/bond. When you click the Pencil tool, the cursor changes to 

resemble a pencil. 

To draw one node bonded to another node: 

1. Place the pencil where you want the first node to appear. 

2. Press and hold the mouse button and drag the cursor to the point 

where you want the second node. Release the mouse button. 

When placing a carbon atom (the default atom), the display of the carbon 

is determined by a setting in the Drawing options of your Structure 

Drawing Preferences. Settings include C, dot, or angle. To change the 

display of carbons for a specific instance, select Carbons from the 

Display menu. 

To change a node: 

1. Click a common atom from the Common Atoms Palette, select 

Atom, Shortcut, Variables, or G-groups from the Draw menu, 

click in the Current Atom box to select an atom, or right-click in 

the Current Atom box to type an atom, shortcut, variable, or G- 

group. 

2. Place the pencil tip on the node that you want to change. An A 

appears inside the pencil when the pencil tip is on a node. Click 

and the node changes to the current atom. 

To change an existing bond: 

1. Click a bond from the Common Bonds Palette to select a single 

or a double bond. Or, display the Bond Selection dialog box by 

selecting Bond from the Draw menu or clicking in the Current 

Bond box. 

☞ If you display the Bond Selection dialog box, click the radio 

button next to the bond that you want and then click Multiple Use 

or Single Use. 

2. Place the pencil tip on the bond that you want to change. A line 

appears inside the pencil when the pencil tip is on a bond. Click 

and the bond changes to the current bond.


Ring Tool 

The Ring tool is used to draw 3 - 15 membered rings. When you click the 

Ring tool, the Ring Description dialog box is displayed. 

Type a number from 3 to 15 to specify the size of the ring you want to 

draw or type a ring system. You may also select the ring size or ring 

system that you want from the scrolling list. A 6-membered ring is the 

default. You may also select one of the common rings by clicking the ring 

icon that you want. 

To draw a ring: 

1. Type a ring size/ring system and click OK or click a ring icon. 

The cursor changes to a 6-membered ring. 

2. Place the ring cursor where you want to insert the ring and click. 

The ring appears in the Structure Drawing window. 

☞ When drawing SPECINFO queries, the rings with alternating 

double and single bonds are drawn with special aromatic bonds. 

Shortcut: To quickly set the Ring tool to the default 6-membered ring, 

right-click on the Ring tool. 

Shortcut: In the drawing area, left-click to place the ring with all single 

bonds. Right-click to place the ring with alternating single and double 

bonds. For example, left-click for cyclohexane and right-click for 

benzene.


Spiro Rings 

To draw a spiro ring system, i.e., two rings that share a single common 

node, create the first ring. Then center the + in the ring cursor directly on 

the node to be shared. Then click. 

Cyclohexane Ring 

Two Cyclohexane Rings 

in a Spiro Ring System 

Fused Rings 

To draw two rings that are fused together, i.e., two rings that share a 

common bond, center the + in the ring cursor on the middle of the bond to 

be shared and click. 

Cyclohexane Ring Two fused Cyclohexane Rings 

Ring Systems 

Type a shorthand ring system description in the Ring Description box or 

select a ring system from the scrolling list. 

A shorthand ring system description includes the number of nodes in each 

ring in the system. By default, rings are fused to one another from left to 

right, e.g., 65 indicates a 6-membered ring fused to a 5-membered ring 

with the 5-membered ring on the right. Ring sizes of 4 through 6 are 

allowed. 

Optional U (Up) and D (Down) indicators modify the direction of ring 

fusion. U moves the location of the fused bond up (counter-clockwise) 

one bond. D moves the location of the fused bond down one bond. 

Additional fusion continues in the new direction until the direction is 

changed. Direction indicators are not allowed when the shorthand 

includes a ring of size 4. 

For example, type 66U6D5 for the steroid ring system.


Then click OK and left-click in the drawing area. 

Chain Tool 

The Chain tool is used to draw chains of lengths ranging from 1 to 30 

atoms. When you click the Chain tool, the Chain Length dialog box is 

displayed. The default chain length is 1. 

Type a number from 1 to 30 or select a number from the scrollable list. 

Then click OK. Your cursor changes to resemble a chain. 

To draw a chain, place the chain arrowhead where you want it to appear 

and click your mouse button. The chain is inserted into your structure 

drawing. 

To insert a chain of a different size, click the Chain tool again. Enter a 

new chain length in the Chain Length dialog box. Click OK. 

You may attach a chain to another chain or to a ring by placing the 

arrowhead of the chain cursor where you want to attach the chain. Then 

click your mouse button. 

☞ STN Express with Discover! attempts to position the chain logically. If 

the chain could overwrite another atom, an error message is 

displayed and the chain is not placed. 

Shortcut: To quickly choose a chain length of 1, right-click the Chain 

tool on the Tool Palette. Then place your cursor in the drawing area. 

Left-click to place the chain.


Eraser Tool 

The Eraser tool is used to delete an atom or bond from your structure. 

When you click the Eraser tool, the cursor changes to resemble a pencil 

eraser. 

To use the Eraser tool, click its icon. 

To remove an atom, position the tip of the eraser on an atom. An A 

appears in the pencil section of the eraser when the cursor is on an atom. 

Click and the atom and any bonds attached to it are removed. 

To remove a bond, position the tip of the eraser on a bond. A line appears 

in the pencil section of the eraser when the cursor is on a bond. Click 

and the bond is removed. To cause the atoms at the ends of the bond to 

be removed also, select Delete Atoms with Bonds on the Drawing tab of 

Structure Drawing Preferences. 

Selection Tool 

The Selection tool is used to select individual atoms, bonds, or structure 

fragments or entire structures. Selected items may be cut, copied, 

deleted, or assigned attributes. If a shortcut is selected, you may reverse 

it, if applicable. 

When you select the Selection tool, the cursor changes to resemble its 

icon. 

To select a structure or a structure fragment, position the Selection tool 

cursor to the top-left point of the structure. Press and hold your mouse 

button while you drag the mouse in a direction where the structure is 

included in a rectangular box. Then release your mouse button and the 

entire structure or structure fragment is selected. 

To select a single bond or node, place the Selection tool cursor on the 

middle of a bond or on a node. Then click. The bond or node is 

highlighted with the color specified in your Structure Drawing 

Preferences. Refer to the Colors/Fonts Structure Drawing Preferences 

section, in this chapter, for more details. 

To select more than one item, press the Shift key and click simultaneously 

while using the Selection tool. This is useful for selecting several nodes 

and bonds that do not fit within a single rectangle.


Lasso Tool 

The Lasso tool is used to select a structure or segments of a structure in 

a free-hand mode. Once selected, you may move, cut, copy, or delete it. 

To lasso (select) an object, click the Lasso tool. The cursor changes to 

resemble a lasso. Press and hold your mouse button and drag the lasso 

cursor around the structure. A line appears around the structure fragment 

as you drag the cursor. Release the mouse button when the entire 

fragment is enclosed (lassoed). 

To move the lassoed structure fragment, place the lasso cursor inside the 

lassoed area. The cursor changes to a hand. Press and hold your 

mouse button while dragging it to a new location. Release the button and 

the selected fragment is redrawn in the new location. 

To remove the lassoed structure fragment, select Cut or Clear from the 

Edit menu or press your Delete key. The selected fragment is removed 

from the structure. If you select Cut, the structure fragment is removed 

and placed on your clipboard. 

To place a copy of the structure fragment on your clipboard, select Copy 

from the Edit menu. The selected fragment is now in the structure and on 

your clipboard. 

To lasso a single node, align the point of the lasso tail on the node. An A is 

displayed inside the lasso cursor when it is touching a node. Click to 

select the node. The node is enclosed in a small box. 

You may move, copy, cut, or delete a single node just as you would a 

structure. 

Text Tool 

The Text tool is used to add nonsearchable text or labels to your structure 

drawings. When you select the Text tool, the cursor changes to resemble 

an I-beam. 

To enter text or labels to your structure, click the Text tool. Position the 

cursor where you want the text to appear and click. Type the text. To add 

text in a different area, reposition your cursor and click. 

Text is displayed in the system font you are using. 

To change the text font, select Preferences from the Structure Drawing 

Main Menu bar or click the Preferences button if it is on the Structure 

Drawing Toolbar. Then click the Colors/Fonts tab. Deselect the Text 

Font=Atom Font box and then click the Text Font button. A Font dialog 

box is displayed. Change the font as desired. 

To delete text, click the Selection or the Lasso tool. Then select the text. 

Press the Backspace key or select Cut from the Edit menu. You may 

also use the Eraser tool to remove each block of text. 

To relocate text, click the Lasso tool. Select the text you wish to move. 

Then drag the selection to a new location.


Structure 

Drawing Main 

Menu Bar 

The Structure Drawing Main Menu Bar provides the tools necessary to 

create a substance, Markush, or reaction query. 

Keyboard shortcuts are available for some commands. They are 

displayed on the menus to the right of the commands. 

☞ Commands that are grayed are not available for the current 

application. 

The File Menu 

The File menu provides basic structure file and window management 

commands. 

New 

The New command provides four subcommands to open a new, Untitled 

structure drawing window for the following structure formats: 

• Standard 

• SpecInfo 

• WPI 

• Questel 

Open (Ctrl+O) 

The Open command opens an existing structure that was previously 

saved. 

When you select the Open command, a list of saved files is displayed in 

the Open Query dialog box. Highlight a file name to see its structure 

query within this dialog box and to identify what format, e.g., Standard, it 

was saved in. If this is the structure file you want to open, click Open. 

Note that you may open several different file types, e.g., MDL molfiles, 

DARC, by clicking the Files of type pop-up menu. 

☞ You may convert a saved file to a new format by clicking the radio 

button next to a format listed in the Convert to section of the dialog 

box. Converted structures are opened in a new Untitled window. The 

original structure retains its original format.


☞ When importing an MDL rxnfile to STN, i.e., MDL à STN, change 

the *.mol to *.rxn in the Open File Name text box. Refer to Appendix 

E, MDL Molfile Conversion Assumptions, for more details. 

☞ Different version of ISIS/DRAW have different instructions for 

copying structures to the clipboard to import to STN Express with 

Discover!. Refer to your ISIS/DRAW documentation for more details. 

Open File Types 

File 

Example Applications 

Format Extension That Create the Format 

STN Express Structure Query .str STN Express 

Chemical Exchange Format .cxf SciFinder 

DARC .drc Generic DARC 

MDL Molfile .mol ISIS/Draw, ChemDraw, 

ChemWindow 

SMD .smd ChemDraw 

Alchemy .alc Alchemy 

Close 

The Close command closes the current structure query. 

☞ If you close a structure query before you save it, you are prompted to 

save. 

Browse 

Browse allows you to quickly view all of the structure queries you have 

saved in your default folder, i.e., the folder you defined in General 

Preferences (the folders command is located in the Setup menu on the 

STN Express Main Menu bar). 

When you select Browse, the Browsing dialog box is displayed. 

You may view each saved query at your pace by clicking Next or you can 

view them in a continuous fashion by clicking Continuous. You may 

modify a structure by clicking Edit.


Save (Ctrl+S) 

Select Save to save a structure query to the directory of your choice. 

After entering a file name and selecting a file type, click OK. A Saving 


Click a ✓ in a box adjacent to an item in black text. Verify Query is 

selected by default and is recommended to catch any drawing errors 

before you search online. See the Query Verification section, later in this 

chapter, for more details. 

☞ If G-group orientation and Verify Reaction Specifications are 

active and are not selected, the query can only be “Saved 

Unsearchable”. These options must be selected, if available, before 

you upload a query to an online session. 

Save As 

Save As allows you to save a structure with a new file name and a new 

standard file type, e.g., DARC, MDL Molfile, or picture file type, e.g., TIFF, 

Metafile. 

Save As File Types 

File 

Example Applications 

Format Extension That Read the Format 

STN Express Structure Query .str STN Express 

Chemical Exchange Format .cxf SciFinder 

DARC .drc Generic DARC 

MDL Molfile .mol ISIS/Draw, ChemDraw, 

ChemWindows 

SMD .smd ChemDraw 

SMILES .smi Daylight’s software 

PCX image .pcx Paint Shop 

Windows Metafile image .wmf Microsoft Word 

TIFF image .tif Microsoft Word


Page Setup 

Page Setup allows you to set page settings for printing. 

Print (Ctrl+P) 

The Print command prints the current structure. 

Exit 

This command ends your structure drawing session. 

The Edit Menu 

The Edit menu provides standard editing commands.


Draw Menu for 

Structure Drawing 

The Draw menu provides commands to help you create structure 

drawings. Some of the commands have shortcuts, e.g., left-clicking the 

Current Bond box to display the Bond 

Selection dialog box. 

Bond 

Select Bond to display the Bond Selection dialog box. 

Click Single Use to insert the bond once. After inserting the bond, the 

default returns to the previous bond. Click Multiple Use to insert the bond 

and retain it as your default. 

Click Cancel to cancel the request. 

Atom 

Select Atom to display the Dialog Box, Periodic Table, or List of atoms. 

The dialog box that displays is the one selected in the Drawing tab of your 

Structure Drawing Preferences. 

If the Periodic Table is displayed, the atom that is the current default is 

highlighted and some of its atomic and physical properties are displayed 

as well. Click an atomic symbol to select a different atom. It will become 

highlighted and its atomic and physical properties will display. Click 

Multiple Use to insert the atom more than once and to retain it as your 

default node. Click Single Use to insert the atom once. Or click Cancel 

to cancel the request. 

If the Dialog Box is selected, the atoms are displayed in a window. Click 

the radio button next to the atom you want. Then click Multiple Use to 

insert the atom and to retain it as your default node. Click Single Use to 

insert the atom once. Or click Cancel to cancel the request.


If List is selected, the atoms are available in a scrollable list. Scroll to an 

atom and select it or type an atom in the Symbol text box. Then click 

Multiple Use to insert the atom and to retain it as your default selection. 

Click Single Use to insert the atom once. Or click Cancel to cancel the 

request. 

Shortcut 

Select Shortcut to display the Shortcuts dialog box. This dialog box 

displays all available shortcuts for common chemical moieties. 

Click the radio button next to the shortcut you want. Then click Multiple 

Use to insert the shortcut and to retain it as your default selection. Click 

Single Use to insert the shortcut once. Or click Cancel to cancel the 

request. 

A shortcut with a small box next to its radio button indicates a Reversible 

Shortcut. If you select a Reversible Shortcut and you wish to reverse its 

orientation after inserting it in a structure, select the shortcut with the 

Selection tool and then choose Reverse Shortcut from the Display 

menu. 

☞ Shortcuts differ for Questel structure queries. 

Variables 

Select Variables to display the Variable Selection dialog box. This dialog 

box provides a list of the available variable nodes you may insert in a 

structure. 

Click the radio button next to the variable you want. Then click Multiple 

Use to insert the variable and to retain it as your default selection. Click 

Single Use to insert the variable once. Or click Cancel to cancel the 

request. 

☞ The X, M, and Id variables may be excluded from a postion in a query 

by clicking the Exclude checkbox.


Variable Points 

of Attachments 

Select Variable Points of Attachment (VPA) to choose multiple possible 

sites of attachment for a node on a single ring or a ring system. 

For example, use VPA to search for pyridines with a chlorine attached at 

the 2- or 3-position. 

To use VPA: 

1. Build a ring or a ring system and build the substituent as a 

separate fragment. In the example, draw the pyridine ring and a 

chlorine atom. 

2. Click the Selection tool and select the node (Cl in the example) 

that may attach to the ring or ring system. Also, select the atoms 

in the ring where the node may attach. 

☞ Hold the Shift key to select multiple items in your structure 

window. 

3. Select Variable Points of Attachment from the Draw menu. 

STN Express with Discover! draws a “connection” from the 

attaching node to the center of the ring or ring system.


The allowable points of attachment on the ring are shown as dotted lines to 

each ring position. To toggle the display of these attachments, select 

Show VPA from the Display menu. 

Using G-groups 

(Ctrl+G) 

Use G-groups to search for structures that have more than one allowable 

value at a node, e.g., use a G-group to search for a benzene with an N, 

O, S, or methyl attached to a given position. 

Using G-groups reduces the need to create multiple structures. G-group 

definitions can include atoms, shortcuts, variables (STN only), other G- 

groups, or fragments. When using fragments, you must draw the 

fragment and point of attachment first. Then define a new G-group value 

or modify an existing one. 

☞ G-Groups must contain between 2 and 20 items. 

To use a G-group, select G-groups from the Draw menu. The G- 

Group Definitions dialog box is displayed. Select a G-group. Click 

Single Use or Multiple Use. 

Place the Pencil tool cursor on the atom you want to replace with the 

G-group and click. The G-group is represented as G1 (or G2, G3, 

etc.). 

Changing a G-group Definition: Select G-groups from the Draw 

menu to modify a G-group definition. Select a previously defined G- 

group from the list. Click Modify. The G-group Definitions dialog 

box is displayed. Select atoms, shortcuts, variables, G-groups, and/or 

fragments to modify. 

Click each item that you want to deselect and/or click new items to 

add to the definition. Click OK to complete the modification. Then 

click Save.


Defining a New 

G-group 

Select G-groups from the Draw menu to display a G-group Definitions 

dialog box. 

Click New. The Define New G-Group dialog box is displayed. 

The first G-group defined is labeled G1. Up to 20 G-groups can be 

defined and each G-group is numbered consecutively, i.e., G1, G2, 

G3,…G20. 

Click Atoms, Shortcuts, Variables, G-groups, and/or Fragments to 

define the members of the G-group. 

Atoms, Shortcuts, Variables (STN only): When you click the Atoms, 

Shortcuts, or Variables button to use in a G-group, the appropriate dialog 

box is displayed. Select nodes to include in your G-group. The selections 

are listed next to the G-group name, e.g., G1. 

G-groups: When you click G-groups, you may add a previously defined 

G-group to a new G-group. To add a G-group, select a G-group from the 

G-Groups Definitions dialog box. This is only available if you have 

previously defined a G-group. 

☞ 

Questel structures may nest G-groups only 3 levels deeper than the 

main drawing level, may use a G-group only once, and require you to 

create another identical G-group if you want to use the same one 

more than once.


Fragments: To include a fragment as a G-group: 

1. Draw your primary structure and the fragment(s) you wish to include 

in the G-group definition. 

2. Define the Points of Attachment for each fragment. 

Select G-groups from the Draw menu. Select @ point of 

attachment. Click Multiple Use. The @ is displayed in the Current 

Atom box. 

☞ No more than two points of attachment are permitted on a 

fragment. 

Select the atoms in your fragment that will be the points of attachment 

to your primary structure. An @ will display next to the atoms you 

selected. 

3. Define a G-group containing a fragment and use it in a structure. 

Select G-groups from the Draw menu. Click New to display the 

Define New G-Group dialog box. Then click Fragments. The 

G-group Fragments dialog box is displayed.


To select all fragments that have defined points of attachment, 

click Include All Fragments. A ✓ is inserted in the Include This 

Fragment check box. Click OK. The G-group definition is 

shown in the Define New G-Group dialog box. 

☞ You can also pre-select fragments to include in your G-group 

definitions by clicking them with the Selection tool. Then 

click the Include Preselected Fragments button in the G- 

group Fragments dialog box to include them. 

Click Save to create your G-group and return to the G-Group 

Definitions dialog box. Click Single Use or Multiple Use. 

You are returned to your structure query. Click the atom you 

want to replace with the G-group. 

4. Click Save from the File menu to save the structure. 

If the fragments contain two points of attachment, the G-group 

orientation option is active and ✓’ed in the Saving dialog box. 

5. G-group Orientation 

When two points of attachment exist in a fragment that is part of a 

G-group and the G-group orientation is ✓’ed, the Fragment 

Orientation dialog box is displayed. Specify the placement of the 

fragment relative to the other atoms in the primary structure. You 

must perform fragment orientation to create a searchable 

structure for STN or Questel. 

☞ G-group orientation is performed during Fragmentation Code 

generation for WPI structures. 

In the Fragment Orientation dialog box, click Show Fragment 

to show how the fragment’s points of attachment are numbered. 

Click Show Structure to see how the G-group is attached within 

the structure. The G-group and a connecting atom are 

highlighted. Select the fragment’s point of attachment number that 

corresponds to the highlighted node in the structure. Click Select 

to continue saving the structure. 

☞ You must select an orientation for single-atom fragments if 

they have two points of attachment.


[ ]m-n (Repeating 

Groups) 

Use the [ ]m-n command to insert a repeating group into your structure 

query. To create a repeating group: 

1. Draw a structure that will contain the repeating group. 

2. Click the Selection tool and select the nodes that are to become 

members of a repeating group. Refer to the Selection Tool 

section for details on selecting multiple items. 

☞ There must be two attachments to the repeating group that are 

not part of the repeating group. 

3. Select [ ]m-n from the Draw menu to define the selected nodes 

as a repeating group. The Repeating Group Range dialog box 

is displayed. Type the numerical range for the group to repeat 

(0-20 times). 

The group is bracketed and subscripted with the repeating range 

entered.


Delete [ ]m-n 

Delete [ ]m-n is used to remove a repeating group from a structure. To 

delete a group: 

1. Click the Selection tool. Select an atom in the repeating group 

that you want to delete. 

2. Select Delete [ ]m-n from the Draw menu to delete the repeating 

group definition. The atoms in the repeating groups are not 

deleted. Only the brackets and repeating range are deleted. 

Chain Superatoms 

Select Chain Superatoms to insert a chain superatom into a WPI 

structure query only. When you select this command, the Chain 

Superatoms dialog box is displayed. 

Click the radio button next to one of the chain superatoms. Then click 

Single Use or Multiple Use. Insert the chain superatom at the desired 

location in your structure. 

Refer to Chapter 8, WPI Fragmentation Codes, for more details. 

Ring Superatoms 

Select Ring Superatoms to insert a ring superatom into a WPI structure 

query only. When you select this command, the Ring Superatoms 


Click the radio button next to one of the ring superatoms. Then click 

Single Use or Multiple Use. Insert the ring superatom at the desired 


Refer to Chapter 8, WPI Fragmentation Codes, for more details. 

Other Superatoms 

Select Other Superatoms to insert a superatom other than a chain or a 

ring superatom into a WPI structure query only. When you select this 

command, the Other Superatoms dialog box is displayed. 

Click the radio button next to one of the “other” superatoms. Then click 

Single Use or Multiple Use. Insert the “other” superatom at the desired 


Refer to Chapter 8, WPI Fragmentation Codes, for more details.


Square Brackets 

Select Square Brackets to insert brackets around a structure or a 

structure fragment. This is useful when you want to include the structure 

or structure fragment in a word processing application to reference it. 

To enclose a structure or structure fragment, select Square Brackets 

from the Draw menu. Your cursor changes to resemble two square 

brackets. Click and drag the cursor so that the dashed rectangle includes 

the structure to be enclosed. A Brackets dialog box is displayed after you 

release the mouse button. 

Type a number from 1 to 99 in the Text box, i.e., a reference number. 

Click the radio button next to Back or Front to place the number after the 

right-most bracket or before the left-most bracket. Click OK. 

☞ Brackets do not affect search results. 

To delete a set of brackets, use the Eraser tool. 

Fuse Fragment 

Fuse Fragment is used to join two fragments at a node or a bond. To use 

this command: 

1. Click the Selection tool and select the node or bond in the 

fragment that you want to fuse. 

2. Select Fuse Fragment from the Draw menu or click the Fuse 

Fragment button if it is located on your Structure Drawing 

Toolbar. The cursor changes to two facing arrows. 

3. Place the cursor at the node or bond of the other fragment that 

you are fusing to the first fragment and click. The fragments 

become fused together. 

☞ Depending on the the positions of the nodes and bonds in the two 

fragments, more than one node and bond can be fused.


Template! 

Menu for 

Structure 

Drawing 

The Template! menu contains a collection of predefined structures to use 

when building a structure query. STN Express with Discover! contains a 

variety of templates in the Templates directory. You may also draw your 

own structures and save them as templates. 

To insert a template into your Structure Drawing window, click Template 

from the Structure Drawing Main Menu bar. The Open Template dialog 

box is displayed and lists the templates by their file names. 

Select a template file by clicking a template file name in the scrollable file 

name box. The structure is shown in the lower right hand corner of the 

dialog box. Then click Open. 

☞ Three types of templates are included with STN Express with 

Discover!. They are the .std (Standard) extension, the .ste (Stereo) 

extension, and the .spe (SPECINFO) extension. Standard and stereo 

templates are in the \template\standard directory while SPECINFO 

templates are stored in the \template\specinfo directory. 

The structure for the template you selected is displayed in the Template 

dialog box and the Selection tool is activated. Select the entire structure 

or a structure fragment and then click OK. 

The Template dialog box disappears and you are returned to the Structure 

Drawing environment. Click to insert the selected structure. 

QueryDef 

Menu for 

Structure 

Drawing 

The QueryDef menu is used to define very specific and precise attributes 

in your structure query, e.g., an STN ring system to be isolated as 

opposed to isolated or embedded. 

☞ To set an attribute for a structure, click the Selection or Lasso tool. 

Select one or more nodes in the fragment to define. Then select a 

command from the QueryDef menu. Select the attributes from the 

resulting dialog box. Click OK. 

Shortcut: To set attribute values on a single atom or bond, right-click on 

that object and select the desired attribute from the pulldown menu.


Ring Isolation 

Ring Isolation is used to select a ring system specification for a selected 

ring. First select the entire ring system or any nodes in it. Then select 

Ring Isolation from the QueryDef menu. The Ring Isolation dialog box 

displays. 

☞ Shortcut: right-click on a node and select Ring Isolation. 

Click the radio button next to the selection you want. The selections 

include: 

• Isolated/Embedded: This setting retrieves search results with the 

selected ring system either isolated or embedded in a larger ring 

system. This is the default and will retrieve the most answers. 

• Isolated: This setting retrieves only search results that have no 

additional ring fusion to the selected ring system. Additional chain 

substitution is allowed at nodes in the ring. 

• Mixture: Structure Drawing activates this choice to remind you 

that you have selected rings or ring systems that have a mixture of 

Ring Isolation settings. You may not select this choice yourself. 

Click OK. 

Bond 

Characteristics 

Bond Characteristics is used to set a bond type and a bond value for one 

or more bonds in a structure query. Select the bonds to be modified. 

Select Bond Characteristics from the QueryDef menu. The Bond 

Characteristics dialog box is displayed and includes options to set the 

Bond Type (ring or chain) and the Bond Value (bond order, e.g., single 

or double). 

☞ Shortcut: right-click on a bond. 

Click the radio button next to the Bond Type and Bond Value that you 

want. Click the Bond Types button to select a bond default for single or 

multiple use. Then click OK. The bond types and bond values include: 

• Bond Types 

Chain: Search results include structures containing only the 

selected bonds in a chain. This is the default type for drawn 

chain bonds. You cannot alter the bond type of bonds drawn in 

rings. 

Ring/Chain: Search results include structures containing the 

selected bonds in either rings or chains. Nodes on either side of 

a bond set to ring/chain are set to ring or chain. 

Ring: Search results include substances containing the specified 

bonds in rings. This is the default type for ring bonds. You may 

change a chain bond to a ring bond, but you cannot alter a bond 

within a drawn ring. The nodes on either side of the new ring 

bond are also set to ring. 

Mixture: Structure Drawing activates this choice to remind you 

that you have selected bonds that have a mixture of bond types. 

You may not select this choice yourself.


• Bond Values 

Exact/Normalized: Search results match answers either with the 

exact bond value drawn or with normalized bonds in the 

corresponding position. Using these bonds ensures maximum 

recall without sacrificing precision. 

Exact: Search results exactly match the bond value drawn. This 

is the default value for carbon-carbon bonds in chains and most 

bonds in isolated rings. 

Normalized: Search results only match answers with corresponding 

normalized bonds. This is the default for even-numbered 

rings and ring systems with alternating single and double bonds 

all the way around the cyclic path and for tautomeric bonds. 

Unspecified: Search results have any bond value for a bond with 

this value. This is selected when the selected bond has a value of 

Unspecified, but is grayed because it is not user-selectable in this 

dialog box. Select Bond from the Draw menu to change bonds to 

Unspecified. 

Mixture: Structure Drawing activates this choice to remind you 

that you have selected bonds that have a mixture of bond values. 

You may not select this choice yourself. 

Click OK. 

Node 

Characteristics 

Node Characteristics is used to set an attribute for one or more nodes in 

a structure query. Select the nodes. Then select Node Characteristics 

from the QueryDef menu. The Node Characteristics dialog box is 

displayed. 

☞ Shortcut: right-click on a node and select Node Characteristics. 

Click the radio button next to the attribute you want. They include: 

• Chain: This setting retrieves search results that include 

structures with the selected node in a chain. This is the default 

for nodes drawn in chains. This characteristic may not be 

applied to a node in a ring. 

• Ring: This setting retrieves search results that have the selected 

node in a ring. This is the default for ring nodes. You may 

change a chain node to ring, but you cannot change a ring node 

to chain. Changing node characteristics of atoms on both ends 

of a bond does NOT change the bond type. 

• Ring/Chain: This setting retrieves search results that have the 

selected node(s) in either a chain or a ring. 

• Mixture: Structure Drawing activates this choice to remind you 

that you have selected nodes that have a mixture of node 

characteristics. You may not select this choice yourself. 

Click OK. 

Changing the node characteristics changes all selected nodes 

regardless of their previous setting.


Hydrogen 

Attachments 

Hydrogen Attachments is used to specify the number of hydrogens 

attached to selected nodes in a structure query. Select the nodes. Select 

Hydrogen Attachments from the QueryDef menu. The Hydrogen 

Attachments dialog box is displayed. 

☞ Shortcut: right-click on a node and select Hydrogen Attachments. 

Select the radio button next to the value you want. 

• Any: This setting retrieves search results that include structures 

with any number of hydrogen attachments at the selected node, 

including none. This is the default setting for all nodes. 

• Specific: This setting allows you to specify the number of 

hydrogens allowed to attach to a selected node. You may specify 

the exact or minimum number. Type a number from 0 to 99. 

Exact: This setting retrieves search results that include only 

structures with exactly the specified number of hydrogens 

attached to the selected node(s). 

Minimum: This setting retrieves search results that include 

only structures with at least the specified number of 

hydrogens attached to the selected node. Alternately, you 

could draw the hydrogens on the node directly using the 

Pencil or Chain tool. 

Mixture: Structure Drawing activates this choice to remind 

you that you have selected nodes that have a mixture of 

hydrogen attachments. You may not select this choice 

yourself. 

The value for hydrogen attachments must include the count of hydrogen 

atoms drawn as attachments to the node. If the value for hydrogen 

attachments is less than the count of hydrogens attached to a node, a 

warning comes up during Save. 

Changing the number of hydrogen attachments changes all selected 

nodes regardless of their previous setting. 

Click OK.


Non-H 

Attachments 

Non-H Attachments is used to specify the degree of substitution for one or 

more selected node(s) in a structure query. Select the nodes. Select 

Non-H Attachments from the QueryDef menu. The Non Hydrogen 

Attachments dialog box is displayed. 

☞ Shortcut: right-click on a node and select Non-H Attachments. 

Select the radio button next to an attribute in the Non Hydrogen 

Attachments dialog box. 

• Any: This setting retrieves search results that include structures 

with substitution of any number of ring or chain non-hydrogen 

connections at the selected node(s). This is the default setting for 

all nodes. 

• Specific: This setting allows you to specify the number and type 

of non-hydrogen connections allowed to attach to a selected 

node. You may specify the exact or minimum number. Type a 

number from 1 to 16. You may specify that the bond(s) to the 

attached node(s) be Chain, Ring, or Ring/Chain. 

Click OK. 

Exact: This setting retrieves search results that include 

structures with only the exact number of Non-H connections 

for the specified type (chain, ring, or ring/chain) attached to 

the selected node(s). 

Minimum: This setting retrieves search results that include 

structures only with at least the specified number for Non-H 

connections of the specified type (chain, ring, or ring/chain) 

attached to the selected node. 

Maximum: This setting retrieves search results that include 

structures with only no more than the specified number of 

non-hydrogen connections of the specified type (chain, ring, 

or ring/chain) attached to the selected node(s). 

Mixture: Structure Drawing activates this choice to remind 

you that you have selected a mixture of non-hydrogen 

attachments. You may not select this choice yourself. 

Chain: This setting defines that the bond(s) to the attached 

node(s) must be chain. 

Ring: This setting defines that the bond(s) to the attached 

node(s) must be ring. 

Ring/Chain: This setting defines that the bond(s) to the 

attached node(s) may be ring or a chain.


Other Attributes 

Other Attributes is used to set a charge, valency, and isotope attributes for 

ONE node in a structure. Select the node. Select Other Attributes from 

the QueryDef menu. The Other Node Attributes dialog box is displayed. 

☞ Shortcut: right-click on a node and select Other Attributes. 

Select the appropriate option from the following: 

• Charge: The default charge is Any, which retrieves answers with 

both charged and uncharged atoms at the selected node. Other 

settings include Any+, Any-, or a specific number in the range 

from -30 to +30. Scroll the Charge box to select a numeric 

charge. 

• Valency: The default valency setting is Any, which retrieves 

answers with any valency on the selected node. Other settings 

include Abnormal or a specific number in the range from 1 to 16. 

Valency is equal to the total number of bonds to a node, plus the 

absolute value of any charge on the selected node. 

• Isotope: The default isotope setting is Any, which retrieves 

answers with any isotope value, including none, for the selected 

node. Other settings include Abnormal or a specific number. 

Specified numbers may be in the range from 1 to 255. 

Generic Definition 

Generic Definition is used to change a default setting for selected generic 

nodes, i.e., Ak, Cb, Cy, Hy. Select a generic node in the drawing area. 

Then select Generic Definition from the QueryDef menu. The Generic 

Definition dialog box is displayed and provides options for Saturation, 

Type of Chain, Number of Hetero Atoms, Type of Ring System, and 

Number of Carbon Atoms. 

☞ Shortcut: right-click on a generic group node. 

☞ Only generic definitions applicable to the selected generic node are 

active.


Click the radio buttons next to the selections you want. Options include: 

• Saturation: A generic group is saturated when all of the bonds 

between the atoms of the group are single exact bonds. The 

generic group is unsaturated when there is at least one double 

exact, triple, or normalized bond in the group. The default setting 

is Any. 

• Type of Chain: A generic group is linear when all of the atoms 

within the group have one or two attachments to other atoms in the 

group. A generic group is branched when at least one atom 

within the group has more than two attachments to other atoms in 

the group. The default setting is Any. 

• Number of Hetero Atoms: A hetero atom is defined as a noncarbon 

atom. Some generic groups may have one or more 

hetero atom. The default setting is Any. 

• Type of Ring System: A ring is monocyclic when only one bond 

must be broken to change the ring to a chain. For polycyclic 

rings, two or more bonds must be broken to change the ring 

system to a chain. The default setting is Any. 

• Number of Carbon Atoms: Selected generic groups may have 

fewer than 7 carbon atoms or 7 or more carbon atoms. The 

default setting is Any. 

Click OK. 

Markush Attributes 

☞ Markush Attributes affect search results only in the MARPAT and 

MARPATPREV Files. 

Markush Attributes is used to change the default setting for one or more 

selected nodes. Select the nodes. Select Markush Attributes from the 

QueryDef menu. The Markush Attributes dialog box is displayed and 

provides options for Match Level and Element Count Level. 


Click the radio buttons next to the selections you want. 

The default may be changed, for rings or chains separately, on the 

Chemistry tab of your Structure Drawing Preferences.


Match Level (MLEVEL) Options 

• Class - searches for structure matches at either the generic group or 

the atom level. This is the initial default setting for chain nodes. 

• Atom - limits the search to structure matches at the atom level. This 

is the initial default setting for ring nodes. 

• Any - searches for matched structures at any level, including generic 

R groups 

• Mixed - Structure Drawing activates this choice to remind you that 

you have selected nodes that have a mixture of match levels. You 

may not select this choice yourself. 

Changing the match level changes all selected nodes regardless of their 

previous setting. 

Element Count Level Options 

• Limited - requires an Element Count to be explicitly stated on 

matching generic nodes in answers. The box is gray if the nodes you 

select have both Limited and Unlimited values. 

After selecting your choices for either Match Level or Element Count 

Level, click OK. 

Element Count 

Element Count is used to limit the types and numbers of elements in 

generic groups or to limit the types of Markush retrievals for your query. 

To use this command, select one or more generic nodes in your structure. 

Then select Element Count from the QueryDef menu. The Element 

Count dialog box is displayed. 


Choose the elements that you wish to limit in your query. Select Exact, 

Range, Minimum, or Maximum. Click Add to apply the Element Count to 

selected nodes. Click Remove to remove the Element Count from 

selected nodes. Click OK to return to structure building. 

If multiple nodes are selected, only the Limited box is available unless all 

of the nodes are generic groups with the same element count definitions. 

The elements available for selection depend upon the generic group 

selected. 

Click ✓ in the Limited box to match generic groups that explicitly meet 

your Element Count specifications. If the Limited box is not clicked, 

generic groups that merely imply your Element Count specification will be 

matched.


Delocalized 

Charge 

Delocalized Charge is used to change the default setting for selected 

nodes. Select the nodes. Selected nodes MUST be adjacent. Then 

select Delocalized Charge from the QueryDef menu. 

The Delocalized Charge dialog box is displayed and provides a scrollable 

list of delocalized charge values. 

Select a delocalized charge from the scrollable list. Options include: 

• Any: Retrieves substances with or without a delocalized charge. 

This is the default. 

• Specific Numbers: Select a specific number between 5+ and 5- 

or a specific number range to include Any+, i.e., from 1+ to 5+, 

or Any-, i.e., from 5- to 1-. 

After selecting a delocalized charge value, click OK. 

Stereochemistry 

Refer to the Stereo Searching section, at the end of this chapter for 

details on this command. 

Free Sites 

☞ The Free Sites command is applicable only when creating WPI and 

Questel structures. 

Free Sites is used to change the default setting for one or more selected 

node. Select the nodes. Select Free Sites from the QueryDef menu. 

The Free Sites dialog box is displayed and provides a scrollable list of 

free site values. 

Select a value from the scrollable list. The default, None, retrieves search 

results containing the normal valency of the atom with hydrogen 

attachments only. 

You may also specify a maximum value, between 1 and 9, for nonhydrogen 

attachments acceptable to the selected nodes. Bond types are 

not considered. 

Click OK.


Review Functional 

Group STN 

Commands 

Review Functional Group STN Commands allows you to review the STN 

command file that represents a saved Functional Group structure query. 

The command file displays the list of search refinement filters that have 

been saved for the query. 

To use this command, select Review Functional Group STN Commands 

from the QueryDef menu. The command file is displayed in the stnedit 

dialog box. 

After you have reviewed the commands, click OK. 

For more details about functional groups, refer to Chapter 7, Reaction 

Queries. 

Query Verification 

Query Verification is used to review the attributes of your current structure 

query. 

To use this command, select Query Verification from the QueryDef 

menu. The Query Verification dialog box is displayed. 

Click the radio button next to All, the default, to review all attributes. 

Or click the radio button adjacent to Select to choose specific attributes to 

review. If you choose Select, you may quickly select attributes in a 

category by clicking the appropriate button, e.g., Rings. Otherwise, click 

a ✓ in each attribute you want to review. 

☞ You may also examine each attribute in a structure query by clicking 

the Query Attribute button on the Toolbar. Refer to the Toolbar 

section earlier in this chapter for more details. 

Click OK. STN Express with Discover! displays small dialogs describing 

these attributes and their locations in your structure.


Display Menu 

in Structure 

Drawing 

Carbons 

The Display menu commands affect the appearance or orientation of 

your current structure. 

Use this option to change the display of individual carbon atoms for the 

purpose of documentation or presentation. Search results are not 

affected. 

First select the carbon atoms that you want to change using the Selection 

tool. Then select one of the three display options available from the 

Carbons command in the Display menu. The selected carbons are 

changed to your specification. 

☞ To change the display of all carbon atoms, click the Carbon Atom 

Display button on your Toolbar or change the setting in the Drawing 

section of your Structure Drawing Preferences. 

Stereo 

Select Stereo to label selected nodes as d, l, dl, “+”, “-”, “+/-”, R, S, RS, 

“.”, “:”, “::”, or RAC. This is for display only and does not affect your 

search results. 

Stereo labels can be deleted using the Eraser tool and moved using the 

Lasso tool. 

Show/Hide VPA 

(STN structures 

only) 

Show Node 

Numbers (N) 

Select Show VPA to toggle the display of hidden “bonds” with Variable 

Points of Attachment. 

Select Show Node Numbers to toggle between showing the node 

symbols, e.g., O, Me, X, or their node numbers. 

Ring Circles 

Select Ring Circles to toggle between displaying benzene rings with a 

circle in the middle or with alternating single and double bonds. 

Show Reactions 

Select Show Reactions to display reaction information such as Reaction 

Roles, Reaction Sites, and Reaction Mapping and to activate the reaction 

drawing tools.


Show Query 

Attributes 

Select Show Query Attributes to launch the query attribute viewer for 

displaying attribute information for a node or bond at the cursor position. 

Smooth (Ctrl+E) 

Select Smooth to straighten and align structure components, e.g., 

freehand drawn rings. 

Sometimes STN Express with Discover! is unable to smooth some 

structures and, in these cases, will display an informational message. 

Also, structures may be “smoothed” in a way that you do not like. If so, 

select Undo from the Edit menu to restore the structure. 

Expand (>) 

Select Expand to enlarge and center your structure drawing. Use the 

scroll bars to view a drawing that is off the screen. 

Contract (


Flip fragment 

vertical (U) 

Select Flip fragment vertical to flip a structure up or down. 

To flip a fragment, position the cursor on an atom on the horizontal axis 

line where the structure will be flipped and click. 

Show Grid 

Select Show Grid to display a drawing grid in your Structure Drawing 

window. The structure is displayed on top of the grid. Refer to the 

Drawing section of Structure Drawing Preferences to modify the 

default spacing between grid lines. 

Snap to Grid 

Select Snap to Grid to place selected nodes on the nearest grid position. 

Refer to the Drawing section of (Structure Drawing) Preferences to 

modify the default spacing between grid positions. 

☞ If no nodes are selected, all nodes in the drawing area are snapped to 

the grid. 

Snap to Compass 

Select Snap to Compass to snap selected bonds to the nearest compass 

position. Refer to the Drawing section of (Structure Drawing) 

Preferences to modify the default spacing between compass intervals. 

☞ If no bonds are selected, all bonds in the drawing area are snapped to 

the nearest compass angle.


Preferences! Menu 

in Structure 

Drawing 

The Preferences! menu is used to customize your Structure Drawing 

environment. Click the Preferences! menu to display the Preferences 

dialog box. 

Six tabs are available to customize structure drawing. They are 

Chemistry, Layout, Save Time, Warnings, Colors/Fonts, and Drawing. 

Click a tab to modify preferences. 

Chemistry 

Click the Chemistry tab to modify defaults for chemistry-related attributes 

in Structure Drawing. 

Click the check box or the radio button to toggle one of the following 

options on or off. 

• Show VPA - select to display right attachment points associated 

with VPA (Variable Points of Attachment). Deselect to hide 

attachment points associated with VPA. This can also be 

changed by clicking the Display menu from the Structure 

Drawing Main Menu bar. 

• Limited - select to set the default for the Markush element count 

level. This may also be changed for any given node with the 

Markush Attributes command or the Element Count command 

in the QueryDef menu from the Structure Drawing Main Menu 

bar. 

• Use Bond Algorithm - allows you to bypass the Structure 

Drawing bond algorithm that automatically sets the bond value for 

optimal retrievals. This creates all bonds as Exact/Normalized 

unless you manually change them. Some queries can be created 

only with the Bond Algorithm turned off. 

• Show Reactions - select to activate reaction drawing mode by 

default.


• Markush Match Level Defaults - select to set defaults for 

Ring Nodes and Chain Nodes when creating Markush 

structures. The defaults may be overridden while in Structure 

Drawing. 

• Methyl Display - choose to display methyl groups as CH3 or 

Me 

Then click OK. Your changes take effect immediately. Click Cancel 

to cancel the changes. 

Layout 

Click the Layout tab to modify display of the Structure Drawing tool 

palette, toolbar, status bar, and tool tips. 

Palette 

Click a ✓ in the check boxes to customize the display of the (Tool) 

Palette. More than one option may be selected. Options include: 

• Horizontal - select to display the Palette horizontally, above 

the Structure Drawing window 

• Visible - select to display the Palette 

• Single Line - select to display the Palette in a single line or a 

double line 

☞ Some Layout changes may not take affect until after STN 

Structure Drawing is restarted. 

Toolbar 

Click a ✓ in the check boxes to customize the display of the Toolbar. 

More than one option may be selected. Options include: 

• Horizontal - select to display the Toolbar horizontally, above 

the Structure Drawing window 

• Visible - select to display the Toolbar 

• Single Line - select to display the Toolbar in a single line or a 

double line


Status Bar 

Click a ✓ in the check boxes to customize the display of the Status Bar. 

More than one option may be selected. Options include: 

• Clock - select to display the current date and time 

• Menu Help - select to display help text for all buttons on the Toolbar 

and the Tool Palette 

• Mol Formula - select to display a saturated molecular formula 

• Tool Tips - select to see information about a tool button when the 

cursor is positioned on a button 

Then click OK to accept all changes. Or click Cancel to cancel the 

changes. 

Save Time 

Click the Save Time tab to customize the features shown in the dialog box 

below. 

• Autosave (Seconds) - automatically saves a query being drawn 

at the time interval specified. Untitled queries are prompted for a 

name, followed by the standard Save options. If you choose to 

cancel this option, you are prompted again, after the specified 

number of seconds, following the next change to the query. 

• Initial Save Dialog Box Checkbox states - click a ✓ in the 

following check boxes to set the initial value at save time. These 

values can be changed at save time, if desired. 

• Query Verify - display the Query Verification dialog box when 

you save a structure query 

• G-group Orientation - prompts you to specify fragment 

orientation for G-groups containing fragments with two or 

more points of attachment 

• Refine Using Structure Filters - Select to refine your 

structure query using structure filters


• Advanced 

• Save all Chain Atoms as Ring/Chain - set all chain atoms to 

Ring/Chain when saved 

• Save all Chain Bonds as Ring/Chain - set all chain bonds to 

Ring/Chain when saved 

• Save all Terminal Atoms as Ring/Chain - set all terminal 

chain atoms to Ring/Chain when saved 

• Select Chain Atoms/Nodes to be saved as Ring/Chain - 

manually select atoms and/or bonds to be saved as Ring/ 

Chain 

Click OK after setting the options. Click Cancel to cancel the 

changes. 

Warnings 

Click the Warnings tab to disable or enable warning messages in 

Structure Drawing. 

To disable messages, select them by clicking anywhere on the line that 

contains each message. Then click Disable. An X appears to the left of 

each disabled message. 

☞ To disable all messages quickly, click the Select All button. Then click 

Disable. 

To re-enable messages, select them by clicking anywhere on the line that 

contains the disabled message. Then click Enable. 

☞ To re-enable all messages quickly, click the Select All button. Then 

click Enable.


If you do not see a message of interest, use the scroll bar to find it. Or 

type words in the Search For > text box. Then click Search For >. If a 

message is found containing the words, it is automatically scrolled to and 

highlighted. 

Click OK after setting the options. Click Cancel to cancel any changes. 

Colors/Fonts 

Click the Colors/Fonts tab to customize the colors of Bonds, Atoms, 

Selections, Attributes, Text, and Reactions and to customize the fonts 

for atom symbols and text. 

To change the color of any item, click the appropriate radio button. Then 

click one of the 16 color boxes. The change is shown in the sample 

structure displayed in the box on the right. 

To change the font for both the atom symbols and the text, click a ✓ in the 

Text Font=Atom Font box (selected by default). Then click the Atom 

Font button. A Font dialog box is displayed. You may change the font 

and point sizes. 

To change the font for the atom symbols or the text, uncheck the Text 

Font=Atom Font box. Then click the appropriate button, i.e., Atom Font, 

Text Font. A Font dialog box is displayed. You may change the font and 

point sizes. 

Click OK after setting the options. Click Cancel to cancel the changes.


Drawing 

Click the Drawing tab to customize the options that affect structures while 

they are being drawn. 

You may modify the following: 

• Double Bond Width (Pixels) - specify the distance between 

double bonds (only takes effect on printing) 

• Pen Width (Pixels) - set the thickness of bonds (only takes 

effect on printing) 

• Grid Spacing (mm) - specify the default distance between 

grid lines. The Grid box must be checked for the Grid to be 

displayed. 

• Compass Interval (deg) - specify the default compass 

interval. (Note that compass intervals used should be factors 

of 90 degrees, e.g., 15, 30, otherwise bonds cannot be drawn 

horizontally and vertically. 

• Bond Length (mm) - set a default bond length which is used 

for the ring and chain commands and for freehand drawing 

when the Snap Bonds option is checked. Snap Bonds must 

be checked to set values for Bond Length. 

• Browse Delay (secs) - set the time between displays when 

browsing structure queries 

☞ Depending on your printer, the double bond width and the pen width 

values may need adjustments. 

You may change the default for display of carbon atoms from Angles to 

Dots or C’s (carbon atoms). 

☞ This is also available by clicking the 

button on the toolbar.


Click a ✓ in any of the following items to turn on the feature. These 

include: 

• Reaction Help (on by default) - display help dialogs when 

drawing a reaction structure query 

• Grid - turns a grid on that acts as a guide when drawing a 

structure. The grid line spacing can be changed using the Grid 

Spacing option. 

• Ring Circles - draw circles inside normalized rings, replacing the 

alternating single and double bonds. Note that refreshing the 

screen display is slower when ring circles are displayed. 

• Snap Bonds - specify the bond length to use when drawing rings 

and chains. Bonds drawn freehand will automatically snap to the 

nearest compass interval at the bond length that you specify. If 

this option is unchecked the standard bond length built into the 

program is used for drawing rings and chains. Bonds drawn in 

freehand are placed at the length and orientation indicated by the 

cursor position. 

• Delete Atoms with Bonds - specify that the nodes at either end 

of a bond are deleted when a bond is deleted 

Click OK after making changes to the Drawing Preferences. Changes 

take effect immediately. Or click Cancel to cancel the changes. 

Building and 

Searching a 

Structure 

Query on STN 

Follow the steps below to build and search the following structure query. 

1. Select Prepare Structure Query from the Query menu or click the 

Prepare Query button on your STN Express Toolbar. 

A new Structure Drawing window is displayed. 

2. Build your structure using the Structure Drawing tools and menus. 

a. Click the Ring tool and click the six-membered hexagonal ring with 

alternating bonds shortcut. Click in the center of your window to 

place the ring.


b. Click the Chain tool and type a 2 in the Chain Length box and 

click OK to draw a 2-length chain. Place the cursor on the lower 

right node of the ring and click. 

Draw a 6-Membered Normalized Ring 

with 2-Atom Chain Attached 

c. Click the Chain tool again. Accept the default chain length of 1 to 

draw a 1-length chain. Click on the upper right node of the ring to 

draw the chain. 

d. Click the double bond icon on the Atoms & Bonds Toolbar to 

select a double bond value for single use. The cursor changes to 

the Pencil tool. Place the Pencil tip on the atom to which you want 

to attach another atom by a double bond. Press the left mouse 

button and hold while dragging the Pencil straight down. Release 

the mouse button to draw a double bond to a single carbon atom. 

Attach an Atom with a Single Bond (Chain Tool) 

and another Atom with a Double Bond (Pencil Tool) 

e. Double click the N icon (nitrogen atom) on the Atoms & Bonds 

Toolbar to select nitrogen for multiple use. Place it on the top 

carbon in the ring and click to replace the carbon with a nitrogen. 

Repeat the process for the bottom carbon in the ring. 

f. Single click the O icon (oxygen atom) on the Atoms & Bonds 

Toolbar to select oxygen for single use. Using the Pencil tool, click 

to place it on the bottom node of the double-bonded chain. 

Add Nitrogen and Oxygen Nodes


g. Select Shortcut from the Draw menu. Select OH and click Single 

Use. Position the Pencil cursor on the right most node in the 

structure and click to replace the carbon with an OH. 

h. Select Variables from the Draw menu and select “X” Halogens. 

Click Single Use. Position the Pencil cursor on the top, right-most 

node and click to replace the carbon with the halogen variable (X). 

This completes your structure drawing. 

Add OH and Halogen Variable (X) Nodes 

3. Select Save from the File menu. Type a name, e.g., halopyra, and 

click Save. Select Verify Query from the Save dialog box. Click 

Save. 

Click OK if each attribute is correct. When the query verification 

completes, you are ready to upload your structure to an online 

system. 

4. Select Exit from the Structure Drawing File menu to return to the Main 

Menu bar 

5. Click the Logon menu to connect to STN, via a logon setup. (Refer to 

Chapter 4, Setup, if you have not defined your setup.) 

STN Express with Discover! opens the STN Terminal Emulation 

window and automatically connects to STN. 

Type FILE REGISTRY at the arrow prompt (=>) and press Return. 

6. Click Upload Structure Query from the Query menu. Click your 

structure file to upload, e.g., halopyra.str, and click Open. 

STN Express with Discover! uploads your structure. 

7. Type DIS QUE (DISPLAY QUERY) and press Return to see the 

uploaded structure diagram.


8. Type SEARCH L1 and press Return. Type the defaults at the search 

type and search scope prompts. 

When the sample search completes, the number of records found is 

displayed, as well as the full file search projections. 

Conduct a Substructure Sample Search (SSS) 

9. Type D (DISPLAY) at the arrow prompt and press Return. The first 

answer from your sample search is displayed. 

Display First Answer of Sample Search 

You can also type D SCAN to display answers in random order. D 

SCAN is a no charge feature that allows you to review answers to 

confirm that you have the expected results from the query.


10. Select Logoff or Logoff Hold from the Online menu. Logoff Hold 

saves your session for 60 minutes with no charge for the hold time. 

Creating 

Stereospecific 

Structures 


Prepare Query button if it is located on the Main Menu Toolbar. Open a 

new or existing file and build and save the structure below. 

Structure Example 

Convert the structure into a chiral structure with the following steps: 

1. Select Bond from the Draw menu. Select Stereo from plane. Click 

Multiple Use to draw more than one Stereo from plane bond. 

2. Click the Pencil tool. Click on the bonds that connect the substituents 

to the ring to make them Stereo. 

Stereo Structure Example 

☞ To confirm that the structure is now a stereo structure, select 

Query Verification from the QueryDef menu. 

☞ To change the orientation, select the node with the Selection tool. 

Select Stereochemistry from the QueryDef menu. Click Invert 

from the Node Attribute list. Click OK.


Stereochemistry 

in QueryDef menu 

Select Stereochemistry from the QueryDef menu to customize your 

stereospecific structure. The Stereochemistry dialog box is displayed. 

The Stereochemistry command is most commonly used to specify either 

Absolute or Relative stereochemistry. The default is Relative. 

Relative searches are broader than Absolute searches because relative 

stereochemistry allows retrieval of both possible enantiomers. When 

performing a relative Stereo Search, your answers may be either absolute 

or relative. The answer record for each substance states whether the 

substance’s stereochemistry is relative or absolute. 

An Absolute Stereo Search limits your answers to the single enantiomer 

that you have drawn in your query. Absolute structure searches reduce 

the number of retrieved records because your search is more precise. 

Also, you may want to set the stereochemistry to Absolute for any query 

with a single chiral center.


To search for structures with double bond geometry, draw the double 

bonds with the geometry that you want. Then indicate that the double 

bond should be searched with stereochemistry by following these steps: 

1. Select the bonds 

2. Select Stereochemistry from the Query menu 

3. Select Stereo under Geometric Bonds in the Stereochemistry 

dialog box 

To further customize structures stereospecifically, select from the following 

options in the Stereochemistry menu. 

• Stereo Set options are used to define different stereo groups 

within a single structure, e.g., to make the relative stereo of the 

attachments to one ring independent of the relative stereo of the 

attachments to another ring. Stereo Sets are typically needed for 

very complex queries. Please consult the STN Help Desk before 

using Stereo Sets. 

• Node Attribute options are used to alter stereo structures, e.g., 

flatten, invert. 

To use any of these options, select the stereo nodes in your structure 

using the Selection tool. Select Stereochemistry from the QueryDef 

menu. Select your options and click OK. 

A Few Hints 

1. The first item drawn in your stereospecific structure is assumed to 

be the stereo center. This determines the direction of all the 

stereo bonds in the structure. 

2. You cannot distinguish whether a stereo query has Relative or 

Absolute stereochemistry by its structure diagram. Queries may 

be checked in STN Express with Discover! by selecting 

Stereochemistry from the QueryDef menu and checking the 

default setting. The text for an answer’s display record will 

indicate whether the stereochemistry is Absolute or Relative. 

3. When creating double stereo bonds and stereo centers, STN 

Express with Discover! automatically checks the bond angles, the 

attachments, the angles of attachments, and the patterns of stereo 

bonds to ensure that the stereo center is valid. Chiral centers 

must unambiguously represent a tetrahedron. If any ambiguity 

exists, an error message is issued. 

4. The small end of a wedge stereo bond must be drawn next to the 

chiral center. To change the direction of a stereo bond, click the 

right mouse button while on that bond.


Stereo 

Structure 

Building 

Features 

The features available in stereo query building are listed in the table below. 

Stereo Query Building 

Function 

STN Express with Discover! Actions 

Change existing bonds to 

stereo bonds 

Select Bond from Draw menu or click Current Bond 

Box to display Bond Selection dialog box. 

Select a stereo bond. 

Create a wedge or dash 

stereo bond 


box to display Bond Selection dialog box. 

Select a wedge or dash stereo bond. 

Delete stereo aspects of a 

stereo bond 


box to display Bond Selection dialog box. 

Select a new bond value.



Function 


“Flatten” a stereo bond 

Select Stereo Mode and choose Stereochemistry 

from QueryDef menu. 

Click flatten. 

Set the stereo default 

Select bond 

Select Stereochemistry from QueryDef menu. 

Select the default option. 

Reverse stereo bond 

Place cursor on stereo bond. 

Click right mouse button on bond. 

Invert a stereo bond 


box. 

Select a different stereo bond. 

Invert stereo bonds from a 

chiral center 

Select stereo node 


Select Invert option. 

Make double bond 

geometric 

Select double bond in structure 


Select choice from Geometric Bonds option.



Function 


Create a Stereo Set 

Select nodes in structure. 


Select option from Stereo Set list. 

Add a node to a Stereo Set 

Redefine Stereo Set. 

Delete a node from a 

Stereo Set 

Select a node. 


Select Node Attribute, flatten, or Stereo Set, none. 

Change the Stereo Set 

type 

Select all nodes in set. Select Stereochemistry from 

QueryDef menu. 

Choose a Stereo Set option. 

Invert stereo in all chiral 

centers 

Click Select All in Stereochemistry from QueryDef 

menu. 

Click Invert . 

Put all chiral centers into 

Stereo Sets 

Click Select All and a Stereo Set choice.



Function 


Delete Stereo at a chiral 

center 

Select the node. 

Select Stereochemistry. 

Select Flatten under Node Attributes. 

Delete stereo aspects of a 

geometric bond 

Select bond in structure. 


Click No Stereo from Geometric Bonds list. 

Delete a specific Stereo 

Set 

Select all nodes in the set. 

Click None from Stereo Set list in Stereochemistry 

from QueryDef menu. 

Delete all stereo 

specifications 


Click Select All, Flatten from Node list, and/or None 

from Geometric Bonds list. 

Delete all Stereo Sets 

Click Delete Sets in Stereochemistry from QueryDef 

menu. 

Delete all geometric 



Click Select All and No Stereo from Geometric 

Bonds list.



Function 


Delete all chiral 



Click Select All and Flatten from Node list. 

Check for common errors 

Select Query Verification from QueryDef menu. 

Select items to verify. 

Click OK. 

Display Stereo Attributes 

and Stereo Sets 

Select Query Verification from QueryDef menu. 

Select items to verify. 

Click OK.


Keyboard 

Shortcuts in 

Structure 

Drawing 

STN Express with Discover! supports many of the standard Windows 

keyboard shortcuts. These shortcuts are listed along with menu 

commands. 

The following shortcuts are available in Structure Drawing and are not 

shown in the menu 

selections. 

Shortcut 

Function 

Backspace (Shift+Del) 

A 

C 

Edit Clear 

Preview Match Level (toggle) 

Chain Tool 

[ Repeating Groups (Draw menu) 

D 

L 

M 

N 

P 

R 

T 

U 

V 

Erase 

Flip Fragment Horizontal 

Center structure 

Show Node Numbers (toggle) 

Repaint 

Ring Tool 

Text input mode 

Flip Fragment Vertical 

Valency of node at cursor 

+ Positive charge dialog for node at cursor


Shortcut 

Function 

- Negative charge dialog for node at cursor 

> Scale up (Expand) 

< Scale down (Contract) 

Ctrl+G 

Ctrl+E 

Right click on bond 

Space Bar 

Right click in Current Atom 

Box 

Right click atom or bond 

Right click common atom or 

bond 

Right click Ring, or Chain 

Tool 

Right click in drawing area 

with Ring or Chain Tool 

Left click on Toolbar or a 

Palette gap 

Right click on Toolbar 

Right click Reaction Arrow 

Right click Text Tool 

G-Groups 

Smooth 

Stereo Bond reversal (in Pencil mode) 

Reset to C and Single Bond (defaults) 

Display the Atom Selection box 

Direct access to attributes 

Change value of common atom or bond 

Select the tool and set the default size 

Insert alternating single and double bonds 

Change the layout of the Toolbar or Palette 

Edit the Toolbar 

Select the tool and the default reaction arrows 

Display font selection dialog


Creating 

Structure 

Queries from 

Structures in 

Transcripts 

STN Express makes it very easy to transform transcript structures into 

searchable structure queries. Just follow these steps. 

1. Select Browse transcript. Open the transcript containing the 

captured structures that you want to change to searchable structure 

queries. 

2. Highlight the structure diagram in the open transcript. Select Create 

Query File from the Edit menu. 

3. The Create Query File message is displayed. Click OK.


4. In the Structure Queries dialog box, type the name that you want to 

assign to the structure.


5. To recall the saved structure, select Prepare Structure Query, select 

File menu, and Open the saved structure.

Reaction Queries 7–1 

7 

Reaction Queries 

The Structure Drawing environment contains reaction and functional group 

drawing tools that enable you to draw reaction queries. Reaction queries 

may include: 

• Structures and roles for the participants 

• A reaction arrow to define the reaction 

• Reaction sites to define the bonds where the reaction takes place 

• Mapping to show the correspondence of atoms in the reactant to 

the atoms in the product 

Reactants, reagents, and products are structure searchable in STN 

reaction files. Catalysts and solvents are not structure searchable. 

To draw a reaction query, you must first open the Structure Drawing 

window by clicking on the Prepare Query button on the main toolbar or 

selecting Prepare Structure Query from the Query menu. Click the 

Reaction button located on the Toolbar or select Show Reactions from 

the Display menu. The Structure Drawing window is displayed in 

Reaction mode and the Reaction Drawing tools are activated. 

☞ To use Functional Groups, you must click the Functional Group 

button. This activates the Functional Group and Reaction structure 

drawing mode drawing tools. 

Rxn Tool Button 

Functional Group Button 

Reaction Drawing Tools 

Functional Group Tools

7–2 Reaction Queries 

Use the Reaction Drawing tools to create your reaction query. 

☞ All Structure Drawing tools that are active are available to draw a 

reaction query. 

Reaction 

Arrow 

Tool 

Click the Reaction Arrow tool from the Tool Palette to set up a chemical 

reaction between structures. A Reaction Arrow dialog box is displayed. 

The first arrow displayed is the default. Click OK to accept the default, or 

select another reaction arrow and click OK. 

To draw an arrow, press the mouse button and drag the arrow between the 

two points where you want the arrow to appear. Release the mouse 

button. You may continue to draw arrows of the same type. To change 

arrow types, click the Reaction Arrow tool again. 

☞ Reaction arrows are not searched. However, if a participant is 

assigned ANY ROLE at the time you draw an arrow, STN Express with 

Discover! reassigns the role as PRODUCT or REACTANT/REAGENT 

based on the direction of the arrow and the proximity of a participant 

to the arrow’s end. 

Reaction 

Role 

Tool 

The Reaction Role tool is used to specify the roles of the participants in a 

reaction. 

To use this tool, click the Reaction Role tool from the Tool Palette. STN 

Express with Discover! displays a message telling you to select a node in 

a structure fragment. Click OK. 

☞ This message is displayed by default. To deactivate all Reaction 

Drawing help messages, access Preferences in Structure Drawing. 

Then click the Drawing tab and uncheck Reaction Help.


Click a node in the structure fragment whose role you want to define. The 

Role Specification Selection dialog box is displayed. 

Select a role. Click OK. 

The role is displayed under the fragment you selected. 

You may continue to specify roles for reaction participants by clicking a 

fragment node, and selecting a role. 

Reaction 

Site 

Tool 

The Reaction Site tool is used to specify a reaction site label for a specific 

bond. Labels include: 

CC - completely changed bond, i.e., the selected bond is either 

formed or broken 

PC - partially changed bond, e.g., an exact bond becomes 

normalized 

XC - either completely or partially changed bond 

NC - the bond is unchanged 

NON - no reaction site specification is declared 

To use this tool, click the Reaction Site tool from the Tool Palette. STN 

Express with Discover! displays a message telling you to select a bond in 

a structure. Click OK. 



Then click the Drawing tab and uncheck Reaction Help. 

The cursor changes to resemble a spider. Click a bond in the structure 

fragment you want to define as a reaction site. The Site Specification 

Selection dialog box is displayed.


Select one of the options. Click OK. 

All reaction sites are marked with the Reaction Site tool cursor symbol on 

the bond. 

☞ If you select the NON site specification, the cursor symbol is removed 

from the bond. 

Atom 

Mapping 

Tool 

The Atom Mapping tool is used to specify a correspondence between 

atoms in the reactant and atoms in the product. 

To use this tool, click the Atom Mapping tool from the Tool Palette. A 


Select either the Manual Mapping or the Automatic Mapping option. The 

default is Manual Mapping. Click OK. 

If you select Manual Mapping, STN Express with Discover! displays a 

message telling you how to use the Manual Mapping. Click OK. 



Then click the Drawing tab and uncheck Reaction Help. 

To indicate a mapping, press and hold the Shift key and click on an atom 

in a structure fragment and then on an atom in another fragment. The 

selected atoms are numbered identically. 

Continue mapping pairs by clicking on the corresponding atoms. Pairs 

are numbered sequentially in the order you map them. 

☞ The elements at both nodes must be the same. Maps may not be 

assigned to shortcut symbols, Gk nodes, or generic groups. 

Select one of the options. Click OK.


Building and 

Searching a 

Reaction 

Query 

Follow the steps below to build and search a reaction query. 

1. Select Prepare Structure Query from the Query menu or click the 

Prepare Query button from the Toolbar. 

2. Click the RXN button located on the Toolbar. 

3. Build the structure shown below using the Structure Drawing tools and 

menus described in Chapter 6, Structure Queries. 

☞ “Any Role” is assigned to all structures in a reaction query 

until you assign them with the Reaction Arrow tool or the 

Reaction Role tool. 

4. Click the Reaction Arrow tool from the Tool Palette. Accept the 

default arrow from the Reaction Arrow dialog box and click OK. 

5. Draw an arrow from the first structure to the second. 

6. The reactions are assigned roles of Reactant/Reagent and Product, 

respectively. 

7. Click the Reaction Role tool from the Tool Palette. Click on a node 

in the first structure. The Role Specification Selection dialog box is 

displayed. 

8. Select Reactant and click OK.


9. Select Save from the File menu or click the Save button if it is located 

on your Toolbar. Type a name, e.g., reactque.str, and click Save. 

10. Query Verification and Verify Reaction Specifications are 

performed to make sure that the query attributes are set to what you 

intended and to ensure all reaction specifications are correct. 

11. Select Exit from the File menu. 

12. Click the Logon menu or click the Logon button from the Toolbar. 

Select a logon setup. (If you have not yet defined a setup, refer to 

Chapter 4, Setup.) 

STN Express with Discover! starts your online session, automatically, 

and opens a Terminal Emulation window. 

13. Type FILE CASREACT, or another reaction file, at an arrow prompt 

(=>) and press Return. 

14. Select Upload Structure Query from the Query menu or click the 

Upload Query button from the Toolbar. Double-click the structure to 

upload, reactque.str. 

STN Express with Discover! displays a dialog box that asks you which 

file you intend to search. 

Select Reaction-searchable file to execute the search in CASREACT 

and to assign a single L-number to the reaction. If you select the 

other options, each structure in the reaction is assigned a separate 

L-number. 

STN Express with Discover! uploads your reaction query, displays a 

dialog box with the status of the upload, and displays the following 

message: Uploading reactque.str. 

15. Type D QUERY and press Return to see the uploaded reaction 

query. 

16. Type SEARCH L1 RANGE=1996 (RANGE is an STN option) and 

press Return. Enter the default at the search type prompt. 

17. Type D (DISPLAY) and press Return. 

The default display format, the first hit reaction, and the compressed 

bibliography for the first answer from your range search are 

displayed.


Structure attributes must be viewed using STN Express query preparation. 

=> SEARCH L1 RANGE=1996 

ENTER TYPE OF SEARCH (SSS) OR CSS: SSS 

RANGE SEARCH INITAITED 12:04:23 

SCREENING 

SCREENING 

SCREENING 

SCREENING COMPLETE - 16517 REACTIONS TO VERIFY FROM 1895 DOCUMENTS 

25.9% DONE 4277 VERIFIED 2 HIT RXNS 2 DOCS 






SEARCH TIME: 00.02.33 

L2 

18 SEA RAN=(1996) SSS L1 

( 25 REACTIONS) 

Select Logoff from the Online menu or click the Logoff button from the 

Toolbar.


Using 

Functional 

Groups 

To use Functional Groups in a Reaction Query, you must open a new 

window by selecting New/Standard from the Structure Drawing File 

menu or clicking the New/Standard button located on the Toolbar. 

After opening a new Structure Drawing window, click the Functional 

Group button on the Toolbar. The reaction and the functional group 

drawing tools, located at the bottom of the Tool Palette, are activated. 

☞ The Ring and Chain tools become inactive in the Functional Group 

mode. 

Selecting a 

Functional Group 

To select a functional group, either: 

1. Right- or left-click in the Current Atom box 

The Functional Group Selection dialog box is displayed. 

Scroll the list to select the Functional Group you want to insert. 

Then click Multiple Use to insert it more than one time and retain 

it as your default. Or click Single Use to insert it one time. The 

functional group you select is placed in the Current Atom box. 

2. Click the Functional Group button on the Tool Palette to select a 

functional group from a predefined list.


Select a Functional Group from any scrollable list. The functional 

group you select is placed in the Current Atom box. 

☞ Functional Groups selected in this manner can only be placed once. 

If you want to select a functional group for multiple use, you must 

right- or left-click in the Current Atom box. See the previous step for 

details. 

Placing Functional 

Groups 

To place a functional group, click the Pencil tool. Then position the Pencil 

tool cursor where you want the functional group and click. 

Continue selecting and placing functional groups until your query is 

complete. 

☞ To see the attributes of a functional group right-click on a functional 

group. Its attributes are displayed in a Functional Group dialog box. 

Completing a 


Reaction Query 

To complete the query, click the Reaction Arrow tool from the Tool 

Palette. Select an arrow from the Reaction Arrow dialog box. Refer to 

the Reaction Arrow Tool section for more details. 

Then click the Reaction Role tool to specify the roles of the participants in 

the functional group query. STN Express with Discover! displays a 

message telling you to select a node in the appropriate fragment. Click 

OK. 



Then click the Drawing tab and uncheck Reaction Help.


The cursor changes to resemble an arrow. Click a functional group. The 

Functional Group Role Selection dialog box is displayed. 

Click the radio button next the role you want for the selected functional 

group. Then click OK. 

☞ Functional Group searching provides additional role values that are 

not available for regular reaction searching. 

Continue assigning roles to the remaining functional groups in the same 

manner. 

To see the structure of a functional group, right-click on the functional 

group name in the Structure Drawing window. The Functional Group 


The name and the structure of the functional group you clicked is 

displayed. Click OK to close this box and return to the Structure Drawing 

window.


Combining 

Functional Groups 

for Searching 

To combine functional groups with the OR Boolean operator within a 

reaction query, click the OR tool from the Tool Palette. 

Position the cursor close to the functional groups that you want combined. 

Press your mouse button and drag until a box encloses those functional 

groups. Then release your mouse button. 

The functional groups are enclosed in brackets and are OR’d together in 

the reaction query. 

When you save a functional group reaction query, an STN Command File 

is also created. Select Review Functional Group STN Commands from 

the QueryDef menu or click the Review FG button from the Toolbar to 

display the stnedit dialog box. 

This identifies the command file that will be used when searching the 

CASREACT File on STN.


Saving a 


Reaction Query 

Save the functional group reaction query by clicking Save from the File 

menu or by clicking the Save button if it is located on the Toolbar. Type a 

file name, e.g., fg2, and click Save. 

Verify Reaction Specifications is performed to ensure all reaction 

specifications are correct. 

Searching a 


Query 

1. Click the Logon menu or click the Logon button from the Toolbar. 

Select a logon setup. (If you have not yet defined a setup, refer to 

Chapter 4, Setup.) 

STN Express with Discover! automatically starts your online session 

within a Terminal Emulation window. 

2. Type FILE CASREACT, or another reaction file, at an arrow prompt 

(=>) and press Return. 

3. Select Upload Structure Query from the Query menu. Double-click 

the structure to upload, fg2.str. 

STN Express with Discover! then uploads the STN FG command file. 

4. Type SEARCH L1 and press Return. 

5. Type D (DISPLAY) and press Return. 

=> S L1 

L2 

2110 NITRO/FG.FORM 

22351 PRIMARY AMINE/FG.RCT 

18565 SECONDARY AMINE/FG.RCT 

554 NITRO/FG.FORM (L) (PRIMARY AMINE/FG.RCT 

OR SECONDARY/FG.RCT 

=> D 

L2 ANSWER 1 OF 554 CASREACT COPYRIGHT 1996 ACS 

6. Select Logoff from the Online menu.

8 

WPI Fragmentation Codes 8–1 

WPI Fragmentation Codes 

The procedures for drawing structures and generating a Fragmentation 

Code strategy are described. Fragmentation Codes are generated from 

WPI (World Patents Index) structures for searching in the WPIDS 

(Derwent subscribers) and the LWPI (the WPI learning file) files on STN. 

If you frequently use the WPI features in STN Express with Discover! 

refer to Chapter 3, Main Menu & Toolbar, and to Chapter 6, Structure 

Queries, for details about modifying the STN Express Toolbar and the 

Structure Drawing Toolbar to contain WPI-specific buttons. 

Creating 

a WPIDS 

or LWPI 

Structure 

Query 

To draw a WPI structure, open Structure Drawing. Click Prepare 

Structure Query from the Query menu or click the Prepare Query 

button on your Toolbar. 

Select New/WPI from the File menu or click the Open WPI button, if it is 

located on your Toolbar, to open a new WPI structure drawing window. 

An Untitled *WPI* window is displayed. 

☞ You may also open an existing WPI structure by selecting Open from 

the File menu or clicking an Open button on the Toolbar. Then 

choose a structure file. The structure is previewed. If the structure is 

in a format other than WPI, click the WPI radio button from the 

Convert to list and click Open. 

Use the structure drawing tools and menus to create your structure query. 

Refer to Chapter 6, Structure Queries, for information about these tools. 

WPI Structure 

Drawing 

Conventions 

The following section lists the structure conventions that can be applied to 

WPI structure drawings. Some conventions differ from those applied in 

structures drawn for other structure-searchable files, e.g., normalized/ 

aromatic bonds are not used in WPI structures. 

For most structures, STN Express with Discover! automatically detects 

groups that could have more than one possible representation, e.g., 

tautomeric systems, and generates the correct code. 

Normalization 

Aromatic rings, such as benzene, should be drawn with single and double 

bonds. Normalized bonds are not used when drawing WPI structures.

8–2 WPI Fragmentation Codes 

Tautomeric 

Structures 

STN Express with Discover! automatically generates the correct 

fragmentation codes for tautomeric structures, e.g., keto-enols. If your 

structure contains a free site, the substitution at this site may result in a 

tautomeric structure. When you generate the strategy, this option is 

displayed in the Select Fragments dialog box. Refer to the Generating 

the Strategy section later in this chapter. 

The L9 negation code is generated only for quinones and other 

unambiguous cases. 

Salts 

Inorganic Anion + Inorganic Cation 

Draw these structures as separate ions or with single bonds, e.g., 

Na + Cl - or Na-Cl 

Ca 2+ Cl - or Cl-Ca + or Cl-Ca-Cl 

Organic Anion + Inorganic Cation 

Draw these structures with bonds between the anion and the cation, 

e.g., 

C-CO-O-Na, C-CO-O-Ca + or 

C-CO-O-Ca-O-CO-C 

Inorganic Anion + Organic Cation 

Draw these structures as disconnected ions with a charge, e.g., 

(CH3)4N + Cl - 

Inorganic Acid Addition Salts of Organic Base 

Draw this salt and acid as two separate fragments on the same 

screen. Do not draw explicit hydrogens, e.g., 

C-N Cl (methylamine.HCl) 

Organic Anion + Organic Cation 

The anion and cation are indexed as two separate records. To 

search, treat each component as a separate structure. Create two 

drawings, one for each component. Then, generate two strategies. 

Combine the hit lists with the AND operator and add the salt code 

manually.


Multi-atom 

Anions 

Simple Metal Containing Anions 

Place the charge on the metal atom, e.g., 

O 

O 

Mn 

O 

O 

Simple Non-metal Containing Anions 

Draw multi-atom anions containing no metals, e.g., sulfate, carbonate, or 

phosphate, with bonds between the sulfur and the oxygen, or the carbon 

and the oxygen, or the phosphorus and the oxygen, e.g., 

O 

O 

P 

O 

O 

Zwitterionic or Ampholytic Compounds 

Zwitterionic or ampholytic compounds are indexed as neutral molecules by 

shifting a hydrogen from the positive part of the compound to the negative. 

If this shift is not possible, the positive and negative parts are indexed 

according to the rules that govern individual acids and bases, e.g., an 

onium group is indexed as charged and an ionized organic acid is 

indexed as a free acid. 

 

N + 

O 

O 

S 

 

O 

Charge Separation Canonical Forms 

If there are no mobile hydrogen atoms and charges are on adjacent 

atoms, the bond order is raised and the charge is neutralized, e.g., 

organic azides R-N=N≡N notR-N=N + =N - 

This is not permitted if the bond is a triple bond.


Dative Bonds 

Dative bonds drawn between two nonmetal atoms are represented by a 

double bond, 

e.g., 

N 

O 

Dative bonds are only used between metals and ligands. Refer to the next 

section, Organometallic Complexes, for more details. 

Organometallic 

Complexes 

Draw all metals and ligands in the same screen. Place the charge on the 

cations and inorganic anions. Do not place a charge on an organic 

anions. Neutral ligands are joined to the metal by dative bonds, e.g., 

Cr 

Carbonyls 

Draw carbonyl groups with double or triple bonds, e.g., 

-C=O or -C≡O 

Acetylacetone and Related Complexes 

Draw acetylacetone and related complexes as two separate fragments. 

No bonds should be drawn between the metal atom and the acetylacetone 

group. Therefore, the code for the metal bound to the oxygen of the 

organic group will not be generated. However, this can be added 

manually.


Adjust the valency of the metal atom or apply charge to avoid filling empty 

valencies with hydrogen atoms, e.g., 

O 

V 

 

O 

O 

The structure should be drawn in this way because attaching the 

vanadium to the oxo group would mean that the code for the two oxo 

groups would not be generated. 

Metal Phthalocyanines 

Draw metal phthalocyanine structures with single and double bonds. 

Attach two of the Nitrogens to the metal using dative bonds, e.g., 

N 

N 

N 

N 

M 

N 

N 

N 

N 

Metal-Carbon 

Bonds 

Draw metal-carbon bonds, where the metal is attached to a specific 

carbon atom, as single bonds, e.g., 

C-C-C-C-Li n-butyl lithium 

For more complex systems, refer to the Organometallic Complexes 

section in this chapter. 

Extended 

Structures 

Draw extended structures, e.g., zeolites, according to the rules governing 

salts, e.g., 

O O - O 

Na + Si Al - 

O O


Sugars 

Input cyclic sugar tautomers in acyclic form. Sugar codes (L8) are not 

generated automatically for these compounds. Select Include WPI Other 

Code Concepts from the Query menu to manually select sugar codes. 

STN Express with Discover! automatically detects structures that may be a 

sugar and asks you if you want to apply the L8 Negation Code to your 

strategy during strategy generation. 

Elements and 

Alloys 

Elements that exist in molecular form in the free state are drawn in their 

normal form, e.g., O=O, F-F. However, you may draw elements as single 

atoms with the valency set to 0. Otherwise, empty valencies are filled with 

hydrogen atoms. 

Alloys are indexed as extended structures and are searched using multifragment 

representation. The valencies of the metals are set to zero, with 

no free sites. 

Quinone Diazides 

Draw quinone diazides, e.g., diazonium phenoxide, with no charge on the 

oxygen. Place the charge on the nitrogen. 

O 

N + 

N 

Hydrogen Atoms 

Hydrogen atoms should not be drawn except as values in G-groups. 

Select H as the value of a G-group by clicking on the Atoms button from 

the G-group definition dialog box. 

Select Deuterium and Tritium from the Atoms menu. 

Hydrogen atoms are assumed to fill the empty valencies on atoms. For 

example, an isolated carbon atom is treated as methane because carbon 

has a default valency of 4. To increase the number of hydrogen atoms 

attached to an atom, increase the valency of the atom.


Constructing 

Generic 

Queries 

Superatoms 

If you are creating a generic WPI structure query, you may use 

superatoms, G-groups, and/or Free Sites in your structure drawing. 

In a WPI format structure, superatoms act as predefined generic groups. 

They generate codes for all of the groups or atoms covered in the 

definition. 

Superatoms include: 

ACT Actinide (including actinium) 

AMX Alkali (ne Earth) Metal 

ARY Aryl-Carbocyclic, optionally fused, containing at least 1 

benzene ring 

A35 Group IIIa-Va Metal - Al, Ga, In, Tl, Ge, Sn, Pb, Sb, Bi 

CHE Alkenyl, Alkenylene 

CHK Alkyl, Alkylene 

CHY Alkynyl, Alkynylene 

CYC Cycloaliphatic - Carbocyclic, optionally fused 

HAL Halogen 

HEA Heterocyclic - Aromatic, Monocyclic (5 or 6 ring atoms) 

HEF Heterocyclic - Fused, optionally aromatic 

HEO Heterocyclic - containing metal, halogen or B, Si, P or As 

HET Heterocyclic - Non-aromatic, Monocyclic 

LAN Lanthanide (including Lanthanum) 

MX Metal, any 

TM1 First series transition metals 

TM2 Second series transition metals 

TM3 Third series transition metals 

TRM Transition Metals excluding Lanthanum 

TX O, S, Se, Te 

UX O, S, Se, Te, N 

ZX B, Si, P, As 

For example, a structure containing a CHK (alkyl), generates codes for all 

the possible alkyl chains; a structure containing a HET generates codes to 

retrieve any monocyclic non-aromatic heterocyclic structures.


Placing 

Superatoms 

To place a superatom, follow the steps below. 

1. Select Chain Superatoms, Ring Superatoms, or Other 

Superatoms from the Draw menu. 

A dialog box is displayed for each respective command. 

2. Select a Superatom from the dialog box. Click Single Use to use 

the superatom once or Multiple Use to change it to your default. 

The superatom you choose is displayed in the Current Atom box 

on the Atom & Bond Palette. 

You may also right-click in the Current Atom box and type a 

Superatom or select a superatom from the scrollable list in the 

Atom Selection dialog box. 

To apply attributes to a superatom, you must: 

1. Click the Selection tool located on the Tool Palette. Then select 

a superatom that is in your structure query. 

2. Select Other Attributes from the QueryDef menu. A dialog box 

is displayed that contains attribute options. 

☞ This dialog box varies depending on the superatom you 

selected. 

☞ You may also right-click on the superatom with the Selection 

or Pencil tool and select other attributes from the pop-up list. 

Modify the attributes by clicking an arrow to display the pulldown menu for 

each attribute and selecting the appropriate menu item. Click OK when 

attributes are complete. Click Cancel to cancel the changes.


G-Groups 

G-Groups may be defined as atoms, shortcuts, superatoms, other G- 

groups, and/or as multi-atom fragments. You may insert a G-group before 

or after you define the G-group. 

Drawing a G-Group 

Right-click in the Current Atom box, located on the Atom & Bond Palette, 

to draw a G-group. The Atom Selection dialog box is displayed. Type a 

G-group, e.g., G1. Click Single Use to use it once or Multiple Use to 

make it your default. 

Click the Pencil tool. Place the G-group on a node and click. 

G-groups can be used more than once, but the values of the G-groups are 

not permuted with one another. 

G 1 

G 1 

G 1 

=H,Cl 

For this example, fragmentation codes are generated for an unsubstituted 

ring and a dichloro- substituted ring. Refer to the Generating the Strategy 

section later in this chapter for more details. 

If you define a G-group as another G-group, the values of the G-groups 

are permuted. 

G 1 

G 1 

=G 2 

=H,Cl 

G 2 

Fragmentation codes generated in this example include codes for an 

unsubstituted ring and a monochloro- and dichloro-substituted compound. 

G-Groups - Fragments 

Fragments included in the definition should be drawn on the screen before 

defining the G-group. The attachment point(s) must be indicated on each 

fragment. Single atoms with free sites or attributes should be drawn as 

fragments with 1 or 2 attachment points. To indicate an attachment, you 

must: 

1. Select G-Groups from the Draw menu 

2. Click @ point of attachment. Click Single Use to indicate one point of 

attachment or Multiple Use to indicate more than one. 

3. Click a node to indicate a point of attachment. An “@” symbol is 

displayed at the node. There is a limit of 20 attachment points per 

structure.


☞ No G-group orientation of fragments occurs when you save the WPI 

structure query. The G-group orientation occurs when you generate a 

Fragmentation Code strategy. See the Orienting Fragments section 

later in this chapter for more details. 

G-Groups - Superatoms 

Draw superatoms as single-node fragments, with attachment points. 

G-Groups - Nesting 

Fragments may contain additional G-groups and/or superatoms. Nest up 

to three levels of G-groups. Examples include: 

• G0 = Ph-G1 

• G1 = -C-G2,-C=O 

• G2 = -O-G3,-C=O 

• G3 = H,C,Et 

Notice that the G3 definition cannot contain another G-group because it 

would exceed the three-level nesting limit. 

For more information on defining G-groups, refer to Chapter 6, Structure 

Drawing. 

Displaying a G-Group 

You may display a G-group definition by: 

1. Selecting G-groups from the Draw menu 

2. Selecting Query Verification from the QueryDef menu 

Select Query Verification from the QueryDef menu to display a G- 

group definition. Click the radio button next to Select, at the top of the 

Query Verification screen, to mark those attributes you want to verify. 

Select Contents in the G-group list. Click OK.


Free Sites 

Free sites allow optional substitution on an atom or a superatom. Free 

sites are not assumed on structures and should be applied if you want to 

carry out a substructure search. 

Select an atom or superatom with the Selection tool. Select Free Sites 

from the QueryDef menu. Enter the number of free sites. The number of 

free sites determines the maximum number of neighbors (substituents) 

permitted on that site, regardless of its bond value. 

For example, 

-C 

retrieves: -CH3, -CH2F, -CHO, -CN, etc. 

-C 2 

retrieves: -CH3, -CH2F, -CHF2, -CHO, -CO2H, -CN 

When you generate a fragmentation code strategy for a structure with 

free sites, you are prompted for substitution information at each free site. 

For more information, refer to the Format of Fragmentation Code 

Strategies section in this chapter. 

If your structure contains a free site on 2 or more atoms, it is possible that 

the substituents on these sites may combine to complete a ring. During 

Fragmentation Code generation, you are asked if this is possible for any 

pair of free sites in the structure. 

However, if two free sites are on the same atom in a ring, it is assumed 

that the substituents do not combine to complete a ring. 

For example, the structure below, 

does not retrieve,


You should draw this structure type with a G-group instead of a carbon. 

The G-group is defined as C with two free sites or CYC, ARY, HET, HEA, 

HEF, and HEO. The attributes on the heterocyclic superatoms should be 

“substituent attached to carbon”. This is the default for all heterocyclic 

superatoms except HEO. 

Ph-G1 G1 = C2 

, CYC, ARY, HEA, HET, HEF, HEO 

Other Concept 

Codes 

When generating a Fragmentation Code strategy, you may include nonstructural 

or sugar codes in your search. 

☞ You must save your WPI query to include Other Concept Codes. 

To use this feature, return to the STN Express Main Menu & Toolbar. Then 

select Include WPI Other Code Concepts from the Query menu. The 

Other Code Concept dialog box is displayed. 

☞ The Other Concept Codes window is blank until you make your 

selections. 

Click Select Codes menu in the Other Code Concepts dialog box. 

Continue to make selections. The selected codes are displayed in the 

Current Selection and the Codes 

Selected dialog boxes. 

The codes you select are combined with the AND operator. AND 

operation specifies that all of the codes are present in the structure 

record. Click the AND operator, on the menu bar, to toggle it to the OR 

operator. OR operation specifies that at least one of the fragmentation 

codes is present in the structure record. 

Click Delete Last or Delete All to delete codes from the Codes Selected 

dialog box. Click Leave OCC to leave this environment. You are returned 

to the Main Menu bar.


Click Edit WPI Strategy from the Query menu to edit a strategy. Select a 

structure query file name. STN Express with Discover! warns you if there 

is a current strategy that may be overwritten. 

Generating 

the Strategy 

First, exit Structure Drawing. Save and name your structure file if you 

have not already done so. 

From the STN Express Main Menu & Toolbar, select Generate WPI 

Strategy from the Query menu. An Open WPI Structure dialog box is 

displayed listing the WPI structures. 

Select a file name to preview the structure. Click a ✓ in the Generate 

RIN codes only box to only generate RINs for your WPI structure. 

If you selected a non-structural code or sugar code from Include WPI 

Other Code Concepts, you may include them in your strategy. Click 

Include OCC. If you did not pre-select one of these codes, the Include 

OCC button is unavailable. 

Click OK after completing your selections. 

Orienting 

Fragments 

If fragments contain two attachment points, STN Express with Discover! 

asks you to specify their orientation. The parent structure is displayed 

with the G-group. An atom that the G-group is attached to is highlighted. 

Click the number of the attachment point that you want connected to the 

highlighted atom. Click Select. Select Show Fragment if you want to 

view the fragment.


Structures with 

Free Sites 

If your structure contains free sites, STN Express with Discover! asks you 

to restrict the substitution type at each free site. 

Click the checkmarks out of the boxes that you wish to exclude from your 

WPI strategy. Then click OK. 

☞ The Select Fragments dialog box is displayed for each node that has 

free sites. The choices available for substitution vary with each 

structure. 

If there are free sites present, STN Express with Discover! displays a 

Groups/Codes Included/Excluded From Free Site Substituents dialog 

box allowing you to restrict the type of substitution in the overall structure. 

Basic Group 

Codes 

The Basic Group Codes dialog box is located on the left side of the 

Groups/Codes Included/Excluded From Free Site Substituents dialog 

box. 

Click a ✓ in the Rings Present dialog box to indicate that rings may be 

present in the structure other than those you have drawn. Then specify 

which type of ring may be present. These selections affect the basic 

group codes and multiplier codes included in your strategy. 

Negation Codes 

The Negation Codes are located on the right side of the Groups/Codes 

Included/Excluded From Free Site Substituents dialog box. Notice that 

every choice is pre-selected, i.e., these groups are assumed to be absent. 

Click the ✓ out of a group box to include the possibility that the group is 

present, i.e., to broaden the search. 

Click Deselect All to permit any of these groups in the WPI strategy. 

Click Select All to exclude all groups from the strategy, i.e., to narrow the 

search. 

When you have completed this selection process, click OK. A warning 

message is displayed informing you that the structure has been modified. 

You are asked if you want to generate the fragmentation codes. Click Yes 

to generate the codes.


Selecting SUBs 

A series of messages are displayed as the structural codes are 

processed. When the process completes, a Select Subs dialog box is 

displayed. 

A list of Subs (Subheadings) (M0-M6) is displayed. Select the ones you 

want to search. Then, click OK. Again, a series of messages are 

displayed as processing continues. 

When the process completes, a command file is displayed in the editor 

that lists the fragmentation code strategy. A file name has been assigned 

and the command file has been saved to disk. 

Editing the 

Strategy 

The Fragmentation Code strategy is displayed as an STN command file. 

You may display and edit this file, provided you are cautious of the script 

variables being used. 

Position the cursor on a code and select Code Definitions from the 

Utilities menu to see a definition of a fragmentation code. 

If you have edited the strategy, select Validate Codes from the Utilities 

menu. Check the fragmentation code strategy list for invalid codes. A 

warning message is displayed if invalid codes are found. This only 

detects mistyped codes. It does not check that your strategy was 

formatted correctly. 

Select Save from the File menu to save the strategy. Two files are saved. 

The STN command file using a .SC extension and a strategy control file 

using a .STG extension. The strategy file contains information linking the 

file and the STN command file. 

Printing the 

Strategy 

On the main STN Express Menu Bar, select Print WPI Strategy from the 

Query menu. You may include the WPI structure, the code definitions, 

the fragmentation code strategy, and the negation code definitions by 

selecting these options in the Select Data to Print dialog box.


Uploading the 

Strategy 

Select STN from the Logon menu to search the fragmentation code 

strategy. You are automatically logged on to STN using your STN logon 

setup you created in Chapter 4, Setup. If you did not set up an automatic 

logon, refer to Chapter 4. 

When the logon completes, you will see an arrow prompt (=>). Type FILE 

WPIDS or FILE LWPI at this prompt. Select Run Command file from the 

Query menu. Type the command file name. This file name ends in .SC. 

Select Exit from the File menu to return to the Main Menu & Toolbar. You 

are prompted to save the strategy if you have not previously done so.

9 

SPECINFO Queries 

SPECINFO Queries 9–1 

The SPECINFO File contains spectral data for a representative section of 

organic chemistry, including organometallic substances. 

SPECINFO features five calculation packages that produce different types 

of spectral data. They are: 

Calculation 

Packages 

CHESS 

Definition 

Searches for chemical structures identical or similar to a query structure 

(structure code similarity search) 

COUPCAL 

Estimates coupling constants for a query structure. Calculates and 

displays NMR-spectroscopic data. 

EDSPEC 

Modifies existing spectra or creates new spectra 

GETSPEC 

Searches for spectra similar to a query spectrum 

SPECAL 

Calculates and displays NMR spectra from a query structure

9–2 SPECINFO Queries 

Creating a 

SPECINFO 

Query 


Prepare Query button if it is located on your Structure Drawing Toolbar. 

Then select New/SPECINFO from the File menu or click the button that 

opens a new SPECINFO structure drawing window from the Structure 

Drawing Toolbar. 

You may also open an existing SPECINFO structure query, by selecting 

Open from the File menu or by clicking an Open button for SPECINFO 

queries from the Structure Drawing Toolbar. 

☞ If you open an existing structure that was created in the Standard, 

WPI, or Questel format and change it to the SPECINFO format, the 

structure is automatically converted to a SPECINFO structure. The 

original structure is retained in its original format and you are 

prompted to name the SPECINFO query when you save it. 

Use the commands and tools discussed in Chapter 6, Structure Queries, 

to draw your SPECINFO structure. 

The commands that differ from the STN Standard structure query 

commands are described next. 

Bond 

Command in 

Draw Menu 

Select Bond from the Draw menu to choose a bond value. You may also 

left click the Current Bond box from the Atom & Bond Palette to quickly 

display the Bond Selection dialog box. 

Three bonds are unique to SPECINFO queries. They include: 

• Aromatic 

• CO (Coordination) 

• CP (Coordination in pi-system) 

The remaining bonds are equivalent to those in standard STN structure 

queries. 

Select a bond and click Single Use to insert the bond one time, or 

Multiple Use to make it the default bond. 

The current bond value is displayed in the Current Bond box.

SPECINFO Queries 9–3 

QueryDef 

Menu for 

SPECINFO 

Queries 

The commands available in the QueryDef menu are described next. 

Query Verification is NOT available for SPECINFO structure queries 

because all attributes are visible in the structure. 

Other Attributes 

Select Other Attributes to change the default setting for the charge of a 

selected node. 

The default charge setting is 0 (zero). This setting retrieves substances 

that are both charged and uncharged. 

Delocalized 

Charge 

Select Delocalized Charge to change the delocalized charge default 

setting for selected nodes. 

☞ You MUST select at least consecutive two nodes with the Selection 

tool before selecting this command. 

In SPECINFO queries, a node may exist in more than one delocalized 

charge group. 

The default setting is Any. This setting retrieves substances with or without 

a delocalized charge group. 

Searching a 

SPECINFO 

Query 

After you have created your SPECINFO query, save and name the file as 

you did with STN Standard queries. Refer to Chapter 6, Structure 

Queries. Select STN from the Logon menu to logon to STN online. 

When you have connected to STN, type FILE SPECINFO at the arrow 

prompt (=>). Select Upload Structure Query from the Query menu. 

Upload the structure you saved. 

Type RUN followed by the appropriate calculation package name 

(COUPCAL, SPECAL, or CHESS) and the L-number of the uploaded 

query. Continue responding to prompts. If you do not know the 

response, type a question mark (?). An explanation of the valid responses 

is displayed and you are reprompted for the information.

10 

Managing Transcripts 

This chapter describes 

Managing Transcripts 10–1 

• browsing transcripts 

• printing transcripts 

• viewing images 

• exporting transcripts as RTF files 

• modifying transcripts with transcript filters 

• customizing highlighting in transcripts 

• combining transcripts 

• editing transcripts with the STN Express editor 

Browsing 

Transcripts 

To browse a captured transcript, follow these steps: 

1. Select Browse Transcript from the Results menu on the Main Menu 

bar, or click Browse Transcript on the toolbar.

10–2 Managing Transcripts 

2. In the Transcript File dialog box, select a file name from the list and 

click Open. 

The Show structure queries option is selected. Deselect this option if 

you do not want to have structure queries included in the transcript. 

3. If your transcript contains downloaded images, i.e., TIFF, GIF, or 

JPEG images, answer the prompt whether to view them in context. 

The selected transcript file opens for browsing.


Saving transcripts 

as RTF files 

While you are browsing a transcript, you may save it as an RTF (Rich 

Text Format) file. 

1. Select Save As from the File menu. 

2. The RTF File dialog box opens with the transcripts listed as .rtf files. 

Select the transcript and click Save. 

The saved transcript automatically opens in the program associated with 

.rtf documents.


Printing 

Transcripts 

To print a transcript from the Main Menu window, follow these steps. 

1. Select Print Transcript from the Results menu or from the Main 

Menu Toolbar. 

2. In the Transcript File dialog box, select the file for printing and click 

Open. 

3. Select the specifications in the Page Layout dialog box and enter any 

specifications for your printer. 

Select Print from the File menu to print a transcript from the STN Online 

and Results window while you are browsing a transcript. Select Print 

from the STN Online and Results toolbar to start printing immediately.


Viewing 

Images 

While you are browsing or printing transcripts, TIFF, GIF, or JPEG 

downloaded images are displayed in context if you answer Yes to the 

prompt: 

In addition, you may display any TIFF images separately from the 

transcript text. Follow these steps. 

1. Select View TIFF image from the File menu.


2. A list of TIFF files is displayed in the TIFF File dialog box. Select the 

TIFF file you want to display. 

3. The TIFF image displays in a separate window.


Exporting 

Transcripts 

as RTF Files 

To export a transcript file to an RTF (Rich Text Format) file, follow these 

steps: 

1. Select Export Transcript from the Results menu. 

2. In the Transcript File dialog box, select a file and click Open.


3. In the RTF File dialog box, the transcript name is displayed with the 

.rtf extension. By default, the file is saved to the default transcripts 

folder, but you can direct it to any location on your PC. Click Save. 

The transcript automatically opens in the program associated with RTF 

files. 

Modifying 

Transcripts 

with 

Transcript 

Filters 

You may easily modify an existing transcript using transcript filters. STN 

Express offers five predefined filters. You may also define your own 

filters. 

To customize your transcript with predefined STN Transcript Filters, 

follow these steps: 

1. Select Browse Transcript and open an existing transcript that you 

want to modify.

2. Select Transcript Filters from the File menu. 


3. In the Transcript Filters dialog box, type the name of a new transcript. 

Click Save.


4. In the Specify Filter dialog box, select one of the predefined filters 

from the Load Filter list. 

Predefined Filter 

stn-ans 

stn-cmd 

stn-cmdh 

stn-strs 

stn-tifs 

Result 

a transcript with only answers 

a transcript with only STN commands 

a transcript with only STN commands 

and their results, excluding reactions 

a transcript with only structure graphics 

a transcript with only TIFF images 

5. Click OK in response to the message confirming that your new 

transcript has been created successfully. 

You may also define your own filter. To define your own filter, enter a new 

name in the Filter name box of the Transcript Filters dialog box. Enter 

the parameters for the information to remove. Click the Help button for 

details and examples of how to create customized transcript filters.


Customizing 

Highlighting 

in Transcripts 

In STN Express you can create a list of terms to be highlighted in a 

transcript. Follow these steps. 

1. Select Browse Transcript to open a transcript. 

2. To create a dictionary file with your list of terms, select Edit 

Dictionary from the Edit menu. 

3. In the Dictionary File dialog box, click New to create a new 

dictionary file.


4. In the Edit Dictionary dialog box, type a term that you want 

highlighted in your transcript. Click Add to add it to the dictionary file. 

Continue adding up to ten terms. Terms will be listed in alphabetical 

order and are not case-sensitive. Click the color in which you want 

the terms highlighted. Click OK. Save the dictionary file at the next 

prompt. 

5. To apply the dictionary, select Install Dictionary from the Edit menu. 

In the Dictionary File dialog box, select the dictionary file to apply. 

Click Open. 

The selected dictionary file is applied to the current transcript, i.e., the 

terms that you have added to the dictionary file are now highlighted by 

displaying them in the color that you have selected.


Combining 

Transcripts 

Follow these steps to merge multiple transcript files into one file. 

1. Open any transcript file that you do not want to merge with another. 

While the transcript file is open, select Combine Transcripts from 

the File menu. 

2. The Combine Transcripts dialog box is displayed. Type a new file 

name in the File name box. Click Save.


3. The Select Transcripts to combine dialog box is displayed. Select a 

file that you want to combine and click Copy. The file is moved to the 

Selected Transcripts box. Select another transcript and click Copy. 

You may merge as many files as you need. Click OK to create the 

merged file.


Editing 

Transcripts 

with the STN 

Express Editor 

To edit a transcript file with the STN Express editor, follow these steps: 

1. Select Edit Transcript from the Results menu or the toolbar. 

2. In the Edit Transcript File dialog box, select the transcript file to edit. 

3. The stnedit window is displayed. 

While capturing a transcript as a .trn file, two separate files are 

created: one contains text and the other contains graphics. Only the 

text file is displayed when using the Edit Transcript command. 

However, graphics and TIFF “call-out” lines are displayed in the 

appropriate locations. DO NOT modify these lines. 

In the stnedit window you may use the standard Cut, Copy, and Paste 

commands, as well as the File, Edit, Search, and Help menus. 

The Search menu provides commands to find and replace terms in your 

transcript file. 

Command in 

the Search menu 

Find (Ctrl+F) 

Find Next (Ctrl+F) 

Replace (Ctrl+H) 

Function 

to find a term in the transcript 

to find the next occurrence of your term 

to replace a term in the text with a term of your 

choice


Adding page 

breaks while 

editing transcripts 

You may add page breaks to a transcript while editing. There are two 

ways to do this. 

1. Position the cursor where you want a page break. Press the Ctrl key 

and the letter L simultaneously. 

2. Create a transcript that contains a page break while online by using 

the Start New Page command from the Results menu. 

While offline, edit the transcript containing the page break and copy 

the line to the clipboard. Edit the file to which you want to add the 

page break and paste the line where you want a page break added. 

☞ The page break needs to be on a line by itself and left justified. 

Using an 

alternative editor 

Instead of using the stnedit editor, you may choose to use another text 

editor. To use another editor, enter its path in General Preferences. 

Refer to Appendix A for information on General Preferences. 

If you have entered the path of an alternative editor, the file that you 

choose to edit is opened in that application. 

While editing a transcript in an alternative editor, you may use the 

features of that editor. However, because you must save the file as ASCII 

text, formatting and font assignments are ignored.

11 

Creating Reports and Tables 11–1 

Creating Reports and Tables 

Overview 

This chapter provides step-by-step instructions for creating reports or 

tables with the following STN Express tools: 

Tool 

Predefined Report Tool 

Custom Report Tool 

Table Tool 

Function 

Creates patent reports from transcripts 

Prepares reports including only desired 

transcript data and formatting 

Creates a table of selected data from 

Search results 

The following topics are included in this chapter 

· Creating patent reports 

· Creating custom reports 

· Saving reports 

· Creating tables 

· Saving tables 

Creating 

Patent 

Reports 

Use the Predefined Report Tool to quickly create a formatted patent report 

from a transcript (.trn or .rtf) file. 

Only answers from the patent files or patent-containing files, e.g., CAplus, 

with the PI (Patent Information) field are included in a patent report 

generated by the Predefined Report Tool. 

The content and format of the predefined report may not be modified. To 

create a customized report, use the Custom Report Tool. 

After creating a transcript, follow these steps to create a predefined patent 

report.

11–2 Creating Reports and Tables 

Selecting the 

Predefined 

Report Tool 

Click the Predefined Report Tool button on the toolbar of the STN 

Express Main Menu and the STN Online and Results window. 

You may also access the tool from the Results menu on the STN Express 

Main Menu or from the File menu of the STN Online and Results window.


Selecting 

transcript 

In the Transcript File dialog box, select the transcript file for your patent 

report. Click Open. 

Patent report 

A predefined report is automatically displayed with patent records from 

your transcript.


Creating 

Custom 

Reports 

Selecting the 

Custom Report 

Tool 

Click the Custom Report Tool button on the toolbar of the STN 

Express Main Menu and the STN Online and Results window. 

You may also access the tool from Results on the STN Express Main 

Menu or from the File menu of the STN Online and Results window.


Report Tool 

window 

Custom Report Tool opens the Report Tool window. 

Select from the buttons on the left side of the Report Tool window.


Alternatively, use the Next and Back buttons to move sequentially 

between screens. When selected, each button displays a screen with 

options for you to choose. Once the transcripts are chosen, you can click 

buttons for different screens in any order. 

Button 

Transcript(s) 

Template 

Content 

Highlighting 

Cover Page 

Fields 

Statistics 

Function 

To select one or more transcripts for 

the report 

To select a template for the report 

To define the content of the report 

To define highlighting in the report 

To define the content and format of the 

cover page 

To select the fields from answers 

To define the charts for the report 

The Report Tool window also includes the following buttons on the bottom 

of the window: 

Button 

Save Template 

Finish 

Back 

Next 

Cancel 

Function 

To save a custom template for reports 

To produce the report once all 

selections for content and style have 

been made 

To go back to a previous screen 

To select the next screen 

To cancel the report-generation 

process


Transcript(s) 

This window is displayed when you select the Report Tool or when you 

click the Transcript(s) button in the Report Tool Window. 

The path for the most recently used transcript is displayed by default. 

Click on the Remove button on the right if you do not want to select this 

transcript for your report. 

Click on the Browse to Add button on the right to locate other transcripts. 

The Transcript File folder opens with a list of transcripts for you to 

choose. Select the desired transcript and click Open or browse for other 

file locations. 

Once you select another transcript, you are returned to the Transcript(s) 

window for the Report Tool. You may select multiple transcripts for a 

single report.


Template 

When you click on the Template button of the Report Tool, a list of the 

currently available templates (.prf files) is displayed. Only one predefined 

template - the patent template - is currently available. If you have defined 

and saved other report templates, their names are also displayed in this 

window. 

The Description box shows a summary of the attributes of the selected 

template. 

Report and Table templates display separately. To view both report and 

table templates, choose the All radio button. A Table template may be 

used for a report and vice versa, but attributes that are not applicable will 

be ignored. 

To locate templates that are not in the default Transcripts folder, clock the 

Change Folder button and navigate to that location. 

Click Choose Template to select the highlighted template for this report. 

If no template is chosen, STN Express sends a prompt for verification. 

Click Ignore to continue to define a custom report.


Content 

In the Content window you may select parts of the transcript for your 

report. Click in the appropriate boxes to include this content in your 

report. 

When the Report Tool is used again, the previous content selections will 

be recalled. 

Highlighting


The Highlighting screen shows the following options: 

Highlighting option 

Highlight Hit Terms 

Highlight the Following Terms 

Highlight Terms in this 

Text File 

Result if selected 

Hit-terms are highlighted in red. Select 

the Format button to change the font 

and/or the color of highlighting. To 

remove any hit-term highlighting, 

deselect this option. 

Type the terms to be highlighted. 

Choose Format to change the font and/ 

or color of highlighting. The highlighted 

terms may be any terms in your 

answers. Terms should be separated 

with commas. Multiword terms between 

commas will be highlighted only when 

the entire phrase is present. This 

feature is case-insensitive. 

Highlight a list of terms saved in a text 

file. Browse for a saved file. Choose 

Format to change the font and/or color 

of highlighting. Each line of the text file 

is treated as a phrase. This feature is 

case-insensitive. 

When you select Format, the following options are displayed. If you 

leave blanks in the Font menus, the highlighted text will follow the font 

definitions from the Fields screen for the field in which it occurs.


Cover page 

1. Select STN Express Cover Page if you want to create a cover page 

for your report. 

1. Choose the content of your cover page by selecting from the options 

on the left, e.g., Title. Note that Title, Prepared By, and For may not 

be de-selected. 

2. Choose if you want to center the Title, Prepared By, and For. If you 

do not select this option, all elements of the cover page are leftjustified. 

3. Select the order of appearance of the selected items on the cover 

page by highlighting the item and moving it with the up and down 

buttons. 

If the centered option, e.g., Title, is selected, you cannot change the 

order of the Title, Prepared By, and For.


4. Click on the tab for each desired selection, e.g., Title, to enter or 

modify the existing information and default format for the selection. 

For example, when you click on the Title tab, the default title, consisting of 

the names of the transcripts, is displayed in the default font and size. You 

may modify or replace the text and select the Format button to change the 

font. 

Other items that are automatically filled include: 

• Prepared by (from User Data in Preferences) 

• Date of Search (from the file-creation date) 

• Strategy (from last DISPLAY HISTORY in transcript) 

• Update Information (from databases entered in transcript) 

• Cost (last cost display in transcript).


Fields 

When you select the Fields button on the left, you are guided in selecting 

the fields for your report. 

The available fields are those found in the transcripts. The fields are listed 

alphabetically in the Field Name window on the left. A blank Selected 

Fields window is displayed on the right. 

Use the buttons in the middle of the screen for selecting the fields: 

Button 

Insert 

Insert All 

Rename 

Delete 

Delete All 

Function 

Insert any highlighted fields from the 

Field Name list into the Selected Fields 

list 

Insert all the fields from the Field Name 

list into the Selected Fields list 

Rename a highlighted field from the 

Field Name list 

Delete any highlighted fields from the 

Selected Fields list 

Delete all the fields from the Selected 

Fields list 

For example, you might want to use the Insert All button to select all 

fields, and then use the Delete button to delete any fields that are not 

desired. You may select multiple fields using the Shift and Ctrl keys.


You may also change the order of selected fields by using the Change 

Order buttons on the right. 

You may change the format of any highlighted fields on the right by 

clicking on the Change Font button. The information that displays to the 

right of the Change Font button reflects the properties of the fields in the 

Selected Fields box. 

An example of the final selection for a report is shown. 

Statistics 

This window is used for defining histograms or pie charts in your report. 

You may create up to 3 histograms or pie charts from the transcript as 

part of the report. 

Choose one field for each histogram or pie chart. You may also choose 

to display the graphs at the beginning or at the end of your report.


Saving template 

Click the Save Template button when you want to save the attributes of 

the current report as a template for future use. 

In the Saving a Template dialog box enter the name for your template and 

click Save. 

Generating report 

To generate a custom report, click Finish. The report is displayed.


Editing reports 

To edit a field in a report, follow these steps: 

1. Right-click on the field. 

2. Choose Edit Field 

3. Make the changes 

4. Click OK. 

Inserting 

comments in 

reports 

To insert a comment for an answer, follow these steps: 

1. Right-click on the answer. 

2. Choose Edit Record Comments 

3. Type the comment. 

4. Click OK. 

Comments are visible on .rep files only, and appear when the mouse is 

passed over the Answer Selection Box. 

Saving 

Reports 

You may save a report as the following types of files: 

• STN Express report (.rep) file 

• Rich Text Format (.rtf) file 

• HTML (.htm) file 

• Microsoft Excel (.xls) file 

• ASCII (.txt) file. 

Saving as STN 

Report files 

To save a report as an STN Express Report (.rep file), follow these steps: 

1. Select Save from the File menu in the STN Online and Results 

window.


2. In the Enter Filename dialog box, select the transcript and choose the 

.rep format for the saved file (.rep is the only type of format available 

when you use the Save option). 

Saving reports in 

RTF, HTML, and 

XLS formats 

1. Select Save As from the File menu to save the report in standard 

formats: RTF, HTML, or XLS.


2. In the Enter Filename dialog box, choose the format for the saved file 

and enter or modify the file name. 

Saving marked 

answers in 

custom reports 

1. Each record in the custom report is preceded by a selection box. 

Click on the selection box to mark this record for saving.

2. Select Save Marked Answers from the File menu. 


3. Another Report window opens, showing only the selected answers. 

Once you are certain that it contains the answers you desire, save 

the report by selecting Save As from the File menu and choosing the 

file format.


Creating 

Tables 

To create tables of data from answers in your transcripts, use the Table 

Tool. For example, you may create tables with: 

• substance names, molecular formulas, and structures from the 

Registry file 

• titles, patent assignees, and IPCs from patent records 

• patent numbers, titles, and graphics 

• trademarks and related data from the trademark files EUMAS and 

DEMAS. 

Selecting the 

Table Tool 

To use the Table Tool, follow this procedure. 

1. Click on the Table Tool button . This button is available on the 

toolbar of the STN Express Main Menu and the STN Online and Results 

window. 

You may also access the Table Tool from the Results menu of the STN 

Express Main Menu or from the File menu of the STN Online and Results 

window. 

Table Tool 

window 

The Table Tool window is displayed. To create a table from answers in your 

transcript, select from the buttons on the left side panel of the Table Tool 

window. When selected, each button displays a window with options for 

you to choose.


The Table Tool window contains the following buttons for your use: 

Button 

Transcript(s) 

Template 

Highlighting 

Cover Page 

Fields 

Statistics 

Function 

To select transcripts for the table 

To select a template for the table 

To define highlighting in the table 

To define the content and format of the 

cover page 

To select the fields (from answers 

displayed) to include in the table 

To define the charts 

The Table Tool window also includes the following buttons (on the bottom of 

the window): 

Button 

Save Template 

Finish 

Back 

Next 

Cancel 

Function 

To save a template for tables 

To product the table once all selections 

for content and style have been made 

To go back to a previous screen 

To select the next screen 

To cancel the selections on a screen


Selecting Table 

Tool buttons 

Selecting any of the Table Tool buttons results in the same type of 

interaction as that produced by the same button of the Report Tool. Refer 

to the section on Creating Custom Reports in this chapter for details. 

Fields 

The following example shows only the Fields screen of the Table Tool 

followed by an example of a table that was created. 

Selecting the Row field results in each row being numbered. 

If you choose Answer for the Selected Fields, answer numbers from 

search results will be included in the table.


Generating Table 

Click Finish when you are done. The table is displayed for you to use. 

Editing tables 

You may edit tables by 

• editing cells 

• copying cells 

• deleting rows 

• sorting columns 

Right-click on the cell, row, or column that you want to modify. Select the 

operation from the displayed menu of options. For example, select Delete 

row to delete the row. 

Resizing the 

columns 

To resize the columns in the table 

• place your cursor on a column separator 

• when your cursor changes to resemble a ladder, with left-right 

pointing arrows, hold down the left mouse key and drag the column 

separator to the desired position 

• release your mouse button


Saving Tables 

You may save tables as the following types of files: 

• Excel Files (*.xls) 

• Express Table Files (*.tbl) 

• RTF Files (*rtf) 

• ASCII Text (*.txt) 

• HTML Files (*.htm) 

Follow these steps: 

1. Select Save As from the File menu.


2. The Enter Filename dialog box is displayed. Enter the name of the 

file in the File name box. In the Save as type box, choose the type of 

file for saving.

12 Accounting 

Overview 

Accounting 12–1 

With the Accounting feature of STN Express you can create a report that 

contains estimated online session costs for your STN sessions. You can 

customize the report to show what is reported, in what time frame, and 

how the report looks. In addition, you can easily export the accounting 

information in various formats, e.g., as an Excel file. 

STN Express automatically saves accounting information for STN sessions 

in the file account.dat. 

Viewing 

Accounting 

Reports 

To view the accounting information, follow these steps: 

1. Select Accounting from the Results menu on the Main Menu bar. 

You may also select the Accounting button 

your Main Menu Toolbar. 

if you have added it to

12–2 Accounting 

2. In the Select Account File dialog box, choose an Account file from 

your Uscripts folder. The default file name is account.dat. Click 

Open. 

3. Your online accounting is shown in the STN Accounting window. The 

estimated costs are displayed in a tabular format.


To resize the columns in the table 

• place your cursor on a column separator 

• when your cursor changes to resemble a ladder, with left-right 

pointing arrows, hold down the left mouse key and drag the column 

separator to the desired position 

• release your mouse button 

Customizing 

Accounting 

Table 

You can customize the accounting table by: 

• changing the accounting table parameters, e.g., list the fields to 

include or exclude 

• defining the time span, i.e., the year and months for the report 

Changing the 

accounting table 

parameters 

1. In the STN Accounting window, click on Setup and select Report. 

2. Customize the parameters in the Report Settings dialog box.


Parameter Function 

Field Name 

Font 

Column Width 

Alignment 

Sort Key 

Units 

Selected Fields 

Choose up to 8 fields (columns) to monitor, 

including a blank column that can be used for 

comments, notes, etc. when you export the 

accounting file 

Choose from among a variety of fonts, styles, and 

point size in your report 

Define the width of the selected field 

Indicate the placement of text within each column 

as left justified, right justified, or centered 

Define the primary and secondary sort fields for 

sorting cost information 

Choose the unit of measure for the width of your 

table 

Insert, delete, and change the order of selected 

fields in your table 

Defining the 

date range 

To define the range of dates for your accounting report, follow these 

steps: 

1. In the STN Accounting window, select Date Range from the Setup 

menu. 

2. In the Set Range dialog box, select the year and months for your 

report.


Exporting 

Accounting 

Data 

To export an accounting report, follow these steps: 

1. Select Export from the File menu in the STN Accounting window. 

2. In the Enter Export Filename dialog box, select or enter the following: 

• the file name to represent the exported file 

• the file format for the exported data, e.g., Excel. 

Click Save. 

If you choose the format as Excel Files, the accounting information is 

displayed as a Microsoft Excel spreadsheet, if you have the software 

available on your PC.


Clearing 

Accounting 

Data 

To clear all cost and session information from the accounting file that you 

have opened, select Clear Data File from the File menu. 

This feature does not remove the file, but only erases the data. If you 

would like to save these data for future reference, make a copy of the 

account.dat file before clearing the data file. 

An informatory message appears that requests confirmation of the action.

Appendix 

A 

Types of 

Preferences 

Preferences 

There are three types of Preferences: 

• General 

• STN Online and Results 

• Structure Drawing 

Preferences A–1 

Structure Drawing preferences are described in Chapter 6. Structure 

Queries. This appendix describes the General and STN Online and 

Results preferences. 

In addition, two preferences in the Host Settings window of Setup are 

noted. 

Accessing 

Preferences 

To access all preferences, click the Preferences tool 

Menu toolbar or from the Setup menu of the Main Menu. 

from the Main

A–2 Preferences 

General 

Preferences 

General Preferences is used to: 

• customize default folders for use in STN Express with Discover! 

• customize the display of the Main Menu and Toolbar 

• select the language that STN Express and related programs use for 

the display of menus and buttons 

• specify your own text editor 

The folders defined here are used by default to save or open a file. You 

may choose another folder each time you open or save a file. 

Changing editor 

In General Preferences you may also designate another editor, rather 

than the text editor provided within STN Express. This option lets you take 

advantage of features of other editor packages. Type or paste the 

complete path to the editor program in the Editor box. If this box is blank, 

the STN Express built-in editor is used.


Changing folders 

To change a folder: 

• Click in the text box of the folder you wish to change and type in the 

pathname, or 

• Click in the text box of the folder you wish to change. Then doubleclick 

a folder or drive letter in the folder selection box, located above 

the Set *Path To button, to select the appropriate folder. Click the 

Set *Path To button once the desired pathname is displayed. 

Customizing 

Main Toolbar 

You may also customize the display of the Main Menu and Toolbar by 

clicking the following options: 

Option selected 

Toolbar 

Always on top 

Minimize on use 

Tooltips 

Result 

Display the toolbar buttons in STN 

Express (default) 

Force the Main Menu & Toolbar to 

remain visible at all times 

Minimize the Main Menu & Toolbar 

after accessing an STN Express 

application 

Control whether the main Toolbar 

has tool tips in addition to the text on 

the buttons 

Selecting the 

language 

You may also select the language that STN Express and related programs 

use for the display of menus and buttons. To use Japanese you must 

have a Japanese version of Windows. The language setting takes effect 

as soon as you click OK. Other STN Express programs that are already 

running must be restarted before the language is changed.


STN Online 

and Results 

Preferences 

To access the STN Online and Results preferences, click the Preferences 

tool on the toolbar of the STN Online and Results window or the Main 

Menu toolbar. 

Click one of the tabs to change those preferences. 

Account 

In the STN Account Type box, select the type of account you have and its 

features: 

• Commercial (Full access) - default setting 

• Full Academic - if you have access to STN files under your 

academic program 

• FIZ Academic - if you have access to FIZ discounted files only 

• CAS & FIZ Academic - if you have access only to CAS and FIZ files 

under your academic program 

• BEILSTEIN subscriber - if you have a Beilstein subscription 

• GMELIN subscriber - if you have a GMELIN subscription 

• DERWENT subscriber - if you have a DERWENT subscription 

Under Property Data Databases, select the property databases that the 

Discover! wizards are authorized to access.


Function Keys 

Use the Function Keys tab to define keyboard shortcuts for frequently 

used text strings. 

Up to 18 key combinations may be defined, using Shift F1-F9 and 

Control-Alt F1- F9. 

To define a Shift Function Key, click the radio button next to Shift. Type 

a text string in any of the function key boxes. 

To define a Control-Alt Function Key, click the radio button next to 

Control-Alt. A new list is displayed. Type a text string in any of the 

function key boxes. 

☞ 

Type [cr] at the end of a line to insert a carriage return after each 

string.


Online 

Use the Online tab to customize your online environment. Click in the box 

adjacent to the preferences you want to activate. Then click OK.



Continuous scrolling 

Modifiable Queries 

Use Filters 

Result 

Text and graphics scroll without 

interruption (recommended) 

Uploaded structure queries may be 

modified in the STRUCTURE 

command 

Automatically upload structure filters 

when they are available 

Enable idle time warning Warning message is displayed after 

Logoff no commands are sent to STN for 15 

Logoff Hold 

minutes 

File Transfer 

Long Packets 4000 

File Transfer 

Log Packets 

Reduce CPU usage when Online 

Display international characters 

Logon splash screen frequency 

once per day 

Autoload command history into 


Faster Kermit downloads of TIFF 

images and other files (recommended) 

A log of upload and download 

(Kermit) activity is created. Select 

only on request by STN support staff 

for problem resolution. 

Puts STN Terminal Emulation into a 

passive mode that uses less CPU 

resources when waiting for you to 

enter data. If this option is not 

selected, STN Terminal Emulation uses 

all the idle CPU time on your local 

system, without degrading 

performance of your machine. 

Allows proper display of international 

characters when you are connected 

to an online host that supports those 

characters. This option cannot be 

used if the connection route to the host 

computer requires the use of parity. If 

the data display from your online host 

appears to be corrupt, turn this option 

off. If the problem is resolved, then 

your connection is using parity. 

STN logon splash screen is 

displayed once per calendar day 

Command history for the current 

session is automatically loaded at 

the time you open the command 

window.


Colors/Fonts/ 

Scaling 

Click the Colors/Fonts/Scaling tab to define colors and fonts in your 

online window or Browse Transcript window or for prints; to scale 

structure graphics; and modify TIFF viewer scale settings. 

To change the color of highlighted text or the color of the text you type at a 

prompt, click the radio button adjacent to Highlight text or Prompt text, 

respectively. Then click the color that you want. 

To change the font of text in the online window or browser window or when 

printing, click the Change button in the Display Font box or the Printer 

Font box, respectively. A Font dialog box is displayed. You may modify 

the font and point size. 

☞ 

For display fonts, only fixed-width fonts are available. For print fonts, 

only fixed width printer and True Type fonts are available. 

Proportional fonts are not available because text does not line up 

properly when they are used. 

To change the horizontal or vertical scaling factor for structure graphics, 

click in the entry box. Enter a new scaling factor. The defaults are 1.0 

for both scaling factors. If the two factors are not changed 

proportionately, vertical or horizontal distortion will occur. 

To modify the initial scale used by the TIFF Viewer, click the appropriate 

radio button next to the Full, Half, or Quarter option.

Links 

Preferences A–9



Use a single browser for 

all WWW links 

Launch a new browser 

window for each WWW link 

Override Windows default 

browser 

Change to STNGUIDE when 

jumping to the WWW 

Full-text links 

Use secure ChemPort link 

Return to original file after 

executing STN links 

(not Full-text) 

Enable Links 

Result 

Existing browser window is reused, if it 

is already running. If the browser 

window is not running, STN Express will 

launch the browser (default). 

A new browser window is opened for 

each WWW link, resulting in multiple 

open windows. 

If you have several internet browsers 

installed, this option allows you to 

specify the path to the one that you 

prefer. 

STN Express with Discover! moves 

your online session to the STNGUIDE 

file any time you request a web 

function. When you are ready to 

continue your STN session in another 

file, you have to enter that file. 

Select the STN service center where 

you have your account 

Select for extra security when you click 

Full-text links; may be selected only for 

access to ChemPort from STN- 

Columbus. 

Return to original file after STN links, 

except for Full-text, are executed. 

Selected items are hyperlinked when 

you are logged on to STN.


Postprocessing 

Postprocessing preferences allow you to set preferences related to 

transcripts.



Capture at logon 

Capture as RTF 

Confirm Transcript 

Capture Stop 

Wrap Abstracts in Export 

Use fixed-width fonts on 

non-wrapping fields in 

reports and tables 

Enable Full-Text links in 

reports and exported 

transcripts 

Symbol characters 

Expand abbreviations 

Launch Excel when 

saving as Excel 

Launch Word when 

saving as RTF 

Combine Author and 

Inventor in Reports and 

Tables 

Combine Patent Assignees 

and Corporate Source 

Autosave Transcript 

Default Font 

Result 

Transcript is automatically captured at logon 

(default) 

Transcript is captured in Rich Text Format. 

Confirmation message is displayed if you 

stop capture of transcript (default). 

Text of abstracts is automatically wrapped in 

RTF transcripts (default). 

Tabular STN data, e.g., patent family 

information, line up in reports and tables 

(default). 

Full-text links are preserved in reports and 

RTF transcripts (default). 

Symbols and special characters, e.g., Greek 

letters, display as symbols or special 

characters in reports, tables, and transcripts 

(default). 

CAS standard abbreviations are automatically 

expanded in transcripts, e.g., “oxidn.” is 

expanded to “oxidation” (default). 

Microsoft Excel (the application associated 

with .xls files) is launched when a file is saved 

in Excel format (default). 

Microsoft Word (the application associated 

with .rtf files) is launched when a file is saved 

in RTF (Rich Text Format (default). 

Combine author and inventor data in 

reports and tables. 

Combine patent assignees and corporate 

source in reports and tables. 

Transcript is periodically saved for a specified 

number of minutes, while you are online. 

Click Change to change the default font for 

custom reports, tables, and exported 

transcripts.




Suppress background display 

of Discover! commands 

Histogram in Analyze 

Answers Wizard 

Edit Alert L-number deletion 

warning 

Result 

STN commands generated by 

Discover! wizards are not displayed in 

the session window until the wizard 

function is completed. 

When the Analyze Answers wizard of 

Discover! is used, analyzed results 

are presented graphically as 

histograms. 

Warning is displayed when a deletion 

of an L-number used in an SDI alert is 

requested. 

Return to original file after Online session returns to the original 

closing a wizard file after a wizard function is 

completed. 

Activate uploaded structure 

queries in 

Uploaded structure queries are 

activated in LREGISTRY by default. 

You may select another structuresearchable 

file in which to activate 

uploaded structure queries.


User data 

Under this tab, you can enter data that appear on the cover page of 

reports and tables. This information is also used to identify you when you 

click Request Help on the Help menu in order to send a message to your 

STN Service Center.


Layout 

Use the Layout tab to customize the layout of your STN Online and Results 

window. 

• Status bar - select the items to display in the Status Bar located at 

the bottom of the STN Online and Results window. 

• Show Toolbar - select to show the Toolbar 

• Open Command Window in locked mode - if locked mode is 

selected, you can enter multiple commands in the Command Window 

before sending them to the host. If locked mode is not selected, the 

Command Window opens in Send mode, which sends a command 

directly to the host when a carriage return is pressed.


Cost warning 


Issue cost warning when 

requesting all answers 

using ‘1-’ 

Issue cost warning before 

display commands exceeding 

Issue cost warning before 

search commands exceeding 

Result 

Warning is displayed when a 

Discover! script contains the TOTAL 

display option requesting a display of 

all answers from an answer set. 

A warning is displayed before a 

Discover! script or a wizard would 

exceed the cost limit you have set for 

answer display. 

A warning is displayed before a 

Discover! script or a wizard executes 

a search command that would exceed 

the cost limit you have set.


Host Settings 

Preferences 

There are two preferences located on the Host Settings window in Setup. 

Option 


Close Window at logoff 

Result if selected 

Command Window is opened when 

you logon to STN. 

STN Express session window closes 

after you logoff from STN.

Appendix 

B 

ALCHEMY 

ALCHEMY B–1 

ALCHEMY 2000 is a powerful molecular graphics and computation tool for 

your desktop computer. It features high-performance visualization for all 

types of chemical structures, including proteins, polymers, and small 

molecules. Features in ALCHEMY 2000 include: 

• Molecular Dynamics - A tool where you can examine the vibrational 

motion of the molecules as a function of time. You may also monitor 

distances and angles throughout the run and create dynamic 

playbacks of results for visual insight. Results are returned in a table 

format. Note that a wizard is available to lead you through setting up 

the calculation and data reporting. 

• Conformational Searching - The opportunity to explore 

conformational spaces of flexible molecules to find global minimum 

geometries that satisfy specific distance constraints. Searching may 

be done by specified increments or randomly assigned values in 

selected dihedrals. Note that a Conformational Search Wizard is 

available for your convenience. 

• Intermolecular Interactions - Create an energy function describing 

the interaction of a small molecule at the site of a large molecule and 

minimize it to determine a geometry for the small molecular at this site. 

Use the Molecular Interactions Wizard to lead your through this 

interaction. 

• Internet Helper Application - Use your browser to display molecules 

when they are downloaded to your machine. 

• Build, analyze, and modify chemical models 

• Energy Minimization - A technique of modifying molecular 

coordinates to obtain reasonable, low-energy molecular geometries 

• Fitting - A visual comparison of a series of molecules by matching 

atom pairs in a least-squares fitting routine. The molecular 

geometries are then compared to superimpose the structures. 

• Twisting - An interactive rotation of parts of a molecule about a bond 

to change its conformation with real-time display of distances and 

angles 

• Spacefilling - A depiction of molecular shape by models that display a 

molecule’s surface as defined by its atomic van der Waals radii 

• Ball and Stack Imaging - Depict a molecule as a sphere connected 

by a slender rod 

Contact Tripos, Inc. for additional information about ALCHEMY 2000. 

Tripos, Inc. 

1699 South Hanley Road 

St. Louis, MO 63144-2913 

Phone: 314-647-1099 

800-323-2960 

Internet: http://www.tripos.com/

B–2 ALCHEMY 

About 

CONCORD TM 

CONCORD. Developed by Robert S. Pearlman and associates at the 

University of Texas, is marketed by Tripos, Inc. 

CONCORD is a computer program for rapid, automatic generation of 

high-quality 3D molecular structures. It is capable of generating 

approximate structures for almost all compounds composed of the organic 

elements with connectivity between 1 and 4. 

CONCORD is not intended to provide realistic structures for large 

molecules with high potential flexibility. For example, octadecane or a 

polypeptide is created fully extended rather than in coiled conformations. 

Many CONCORD structures are visually indiscernible from structures 

optimized by Molecular Mechanics (MM) or Molecular Orbital (MO) 

energy. 

CONCORD structures are usually generated in 0.2 to 2 VAX 11/780 CPU 

seconds. Many energy minimizations take several minutes to several 

hours of CPU time. Thus, CONCORD represents a compromise between 

speed and accuracy. Studies indicate the loss in accuracy as very small. 

Diagnostics are provided for those exceptions. 

CONCORD structures serve as exceptionally good initial guesses for 

energy minimization procedures when your application demands such 

accuracy. 

Ring Systems 

A ring system is defined as a set of rings. Each ring in the set contains at 

least two atoms in common with another ring in the set. An analysis of 

each ring system determines the general conformation of each ring. The 

bond and torsion angles are determined by minimizing a strain function. 

CONCORD can construct mono- and polycyclic planar ring systems, as 

well as complex, nonplanar, heteroatomic, fused, bridged, spiro, and 

caged ring systems. A maximum of 200 heavy (non-hydrogen) atoms per 

molecule is permitted. 

The Mechanism 

of Transformation 

The CONCORD algorithm provides a mechanism for transforming the 

information contained in a molecule’s atomic CONnection table into the 

atom CoORDinates. Connection tables from the CAS REGISTRY File for 

organic substances without stereochemistry and standard CAS bond 

conventions are provided to CONCORD. 

The resulting coordinates are available to download using STN Express 

with Discover!. Substances with more than one component or single atom 

fragments, polymers, coordination compounds, or incompletely defined 

substances are not processed.

ALCHEMY B–3 

Energy 

Configuration 

By default, CONCORD produces the lowest energy configuration. It is 

consistent with the connectivity and the stereochemistry of the structure. 

For example, methylcyclohexane and 2-butene are made in the lowenergy 

equatorial and E configurations, respectively. Coordinates are 

unavailable for stereo-specific substances. However, coordinates for 

chiral substances with no stereochemistry (NS) are specified. These 

substances are chiral in nature, but are referred to in literature as having 

no stereochemistry specifications. 

Structure-Building 

Algorithm 

CONCORD’s structure-building algorithm is an offspring of the expert and 

pseudo-molecular mechanics approaches. Decisions regarding bond and 

torsion angles are based on a set of rules that expert chemists apply. For 

example, methoxybenzne is made in the plane of a ring, whereas the 

methyl group in 2,6-dichloromethoxybenzene is oriented perpendicular to 

the plane of the ring. 

Other decisions are made through an optimization procedure to minimize 

the molecular mechanics energy function. Decisions regarding bond 

lengths are based on a table. A warning message is issued when an 

approximated bond length is used. 

Acyclic 

Substructures 

The geometry of acyclic substructures is determined by minimizing steric 

interactions. H-bonding and stereochemical specification calls are 

exceptions for higher energy isomeric forms. 

ALCHEMY 

MOL Files 

The 3D CONCORD structure downloaded from STN Express with 

Discover! is contained in an ALCHEMY MOL File. The MOL File contains 

a complete description of the molecule. The number of atoms, bonds, and 

charges, as well as the atom types, coordinates, and connectivities are 

listed. A comment is also included with CONCORD diagnostics, as well as 

the CAS Registry Number for the substance. 

A portion of an ALCHEMY MOL File may resemble the following: 

16 ATOMS, 15 BONDS 

1 C3 -0.4675 0.0282 0.0633 

2 C3 -1.0699 0.0751 -0.0501 

3 H -0.8919 0.9898 -0.2579 

The first line in the file represents the number of atoms and the number of 

bonds in the molecule. 

Next is a set of lines, one per atom, that provide the atom number, the 

atom label, and the x, y, and z coordinates of the atom, in angstroms. The 

atom number is not read by ALCHEMY. The atom label is four characters 

or fewer.

B–4 ALCHEMY 

The following list of atoms is the bond list, part of which is shown below. 

The first column in this table is the bond number. It is not readable by 

ALCHEMY. The next two numbers are the first and second atoms of the 

bond pair. The last column is a text field describing the bond value, e.g., 

SINGLE, DOUBLE, TRIPLE, or AROMATIC. 

1 1 2 SINGLE 

2 1 3 SINGLE 

3 1 4 SINGLE 

4 1 5 SINGLE 

5 5 6 SINGLE 

The first line indicates that a single bond exists between the first and the 

second atoms in the previous atom list. The next three lines show that the 

first atom is also bonded to atoms 3, 4, and 5. The last line indicates that 

a single bond exists between atoms 5 and 6. 

STN Express with Discover! may potentially add two more fields to the 

MOL File it creates, the CAS Registry Number and the CONCORD 

Diagnostic Message. 

The CAS Registry Number is considered an optional field. It is always 

present in files downloaded from STN. 

The CONCORD Diagnostic Message is also an optional field. Typically, 

these are not present. If it is present, the message “Warning Diagnostic 

generated by CONCORD” is displayed. 

ALCHEMY 

2000 and STN 

Express with 


ALCHEMY 2000 can be used in conjunction with STN Express with 

Discover!. You can: 

1. Search structures created in ALCHEMY on STN by importing 

them into STN Express with Discover! and uploading to a 

structure-searchable file 

2. Download with STN Express with Discover! 3D CONCORD 

coordinates, generated by CONCORD, for over 6 million organic 

compounds from the CAS REGISTRY File for molecular modeling 

with ALCHEMY 2000 

For information about building ALCHEMY structures, refer to your 

ALCHEMY manual.

ALCHEMY B–5 

Searching for 

ALCHEMY 

Structures on 

STN 

ALCHEMY structures are searched on STN as follows: 

1. Transfer a connection table for a structure search 


Prepare Query button if it is located on your Main Menu Toolbar. 

Depending on how you saved your ALCHEMY structure, change the 

Files of Type setting to Alchemy Molfile or MDL Molfile. Select a 

file and click Open. 

Each MOL File contains data, connection tables, and coordinates for 

a single substance. Refer to your ALCHEMY manual for information 

on using MOL Files. 

2. Edit the ALCHEMY structure in STN Express with Discover! 

Edit and modify the ALCHEMY structure that was imported to STN 

Express with Discover!. These structure types are edited and 

modified like any structure created on STN Express with Discover!. 

Refer to Chapter 6, Structure Queries, for more information. 

3. Upload ALCHEMY structures to STN 

Upload the imported ALCHEMY structure from STN Express with 

Discover! to STN to search the STN structure files. 

Refer to Chapter 6, Structure Queries, for information on structure 

searching.

B–6 ALCHEMY 

Downloading 

Answers 

from STN for 

Molecular 

Modeling in 

ALCHEMY 

Search the REGISTRY File on STN to retrieve three-dimensional (3D) 

coordinate data for millions of organic compounds. The data are 

generated by CONCORD. 

Download 3D CONCORD data from STN Express with Discover! by using 

the search answers from the REGISTRY File or by providing Accession 

Numbers. In REGISTRY, the Accession Number is identical to the CAS 

Registry Number. Type HELP ACC at an arrow prompt (=>) for 

information about Accession Numbers in the REGISTRY File or refer to 

the REGISTRY File Database Summary Sheet for overall file information. 

Download connection tables for substances that have 3D CONCORD in 

the REGISTRY File’s 

File Segment (/FS) search field. Use CONCORD/FS to limit your answers 

to those containing CONCORD data. You may download to a local PC or 

to a terminal by typing DOWNLOAD ALCHEMY at an arrow prompt (=>). 

STN Express with Discover! executes Kermit to process 

the file transfer. Choose a file name with a .mol extension. 

For example, inititate the following search in the REGISTRY File: 

=> S ATROPIN? AND CONCORD/FS 

336 ATROPIN? 

5469078 CONCORD/FS 

L1 19 ATROPIN? AND CONCORD/FS 

=> D 

L1 ANSWER 1 OF 19 REGISTRY COPYRIGHT 1996 ACS 

RN 114473-22-2 REGISTRY 

CN Benzeneacetic acid, .alpha.-chloro-, 2-oxo-1-phenyl-2-[(1,2,2,6- 

tetramethyl-4-piperidinyl)oxy]ethyl ester (9CI) (CA INDEX NAME) 

OTHER NAMES: 

CN Eucatropine .alpha. -chlorophenylacetate 

FS 3D CONCORD 

MF C25 H30 Cl N O4 

SR CA 

LC STN Files: CA, CAPLUS, TOXLIT, USPATFULL 

1 REFERENCES IN FILE CA (1967 TO DATE) 

1 REFERENCES IN FILE CAPLUS (1967 TO DATE) 

=> DOWNLOAD ALCHEMY 

ENTER (L1), L#, ACC OR ?:L1 

ENTER ANSWER NUMBER OR RANGE (1):1 

ENTER HIGHLIGHT OR NOHIGHLIGHT:HIGHLIGHT 

ENTER FILENAME OR (?):ATROPINE.MOL 

TEXT DATA WILL BE DOWNLOADED TO ‘ATROPINE.MOL’ USING ‘CAPTURE’ 

START DOWNLOAD (Y):Y

Appendix 

C 

Script Language 

Script Language C–1 

A script is a text file that contains a set of statements in the Script 

Language that are executed by STN Express with Discover! The STN 

Express with Discover! Script Language can be used to create: 

• custom logon procedures 

• custom search strategies 

• procedures to automate repetitive search or display tasks. 

For example, you may routinely perform a certain subject or author 

search on STN. Rather than logging on to STN and opening a transcript 

file to capture search results, searching multiple files, and then logging off 

and reviewing the transcript, you can use scripts to streamline the 

process. One script can log you on to STN, another can initiate the 

searches, and another script can display your answers. Alternatively, one 

script can perform all three tasks. Because the script runs automatically, 

without waiting for you to type, you may reduce your online time and 

costs. 

Steps in 

Writing and 

Running a 

Script 

Defining the Task 

Define what you want to accomplish and the steps required to accomplish 

the task. For example, suppose you have a list of CAS Registry Numbers 

(RN) and want to display their records on STN. What steps would you 

follow? 

1. Log on to STN. 

2. Enter the Registry file. 

3. Display the record for the first RN. 

4. Repeat step 3 until finished. 

5. Log off STN.

C–2 Script Language 

Translating the 

Task into Script 

Statements 

After you have defined the task, translate the steps into Script Language 

statements that will accomplish the task. (The statements are listed in 

detail later in this Appendix.) 

1. Log on to STN. 

The script could log on to STN, but it is often better to separate the 

logon task from the job the script performs. In this example, log on to 

STN as usual and then run the script. 

2. Enter the Registry file. 

The STN command to enter the Registry file is FILE REGISTRY. To 

use an STN command in a script, use the => (arrow prompt) 

statement: 

=> FILE REGISTRY 

3. Display the record for the first Registry Number. 

To display a record on STN, use the DISPLAY command. Again we 

use the => statement: 

=> DIS 50-00-0 

4. Repeat step 3 until finished. 

Add more DIS commands 

5. Log off STN. 

End your STN session with the LOGOFF command, again using the 

=> statement: 

=> LOG Y 

Creating a script 

To create a script, select Prepare Command File from the Query menu 

on the STN Express Main Menu. Click New in the Open Script dialog. 

This opens the STNEdit window with an Untitled text window inside it. 

Type the following script statements: 

\* Display CAS RNs in the Registry file on STN. 


=> DIS 50-00-0 

=> DIS 7777-77-7 

=> LOG Y


Saving the Script 

To save the script file, select Save from the File menu. Type a name in 

the File name box and click Save. By default, the script file is saved to the 

User Scripts folder defined in General Preferences in the Setup menu 

(on the Main Menu Toolbar). Refer to Appendix A for information about 

General Preferences. 

Do not use any name that exists in the Predefined Scripts folder unless 

you are replacing the functions of that script. 

Checking the 

Script for Errors 

To check the script for syntax errors, go to the Utilities menu in STNEdit 

and select Check Command File. If errors are found, STNEdit highlights 

appropriate script lines and displays a message at the bottom of the 

STNEdit window. To learn the nature of the error, move the mouse pointer 

over the highlighted part of a line. Correct the error, save the script, and 

check the script again until no errors are found. 

Check Command File does not find all errors because some errors 

cannot be found until the script actually runs. 

It is not necessary to be logged on to an online host to use Check 

Command File. 

Using or Running 

the Script 

While you are logged on to STN, Select Run Command File from the 

Query menu. A Command File dialog box is displayed. Select a script 

file to run and then click Open. The script runs until it finishes or until an 

error is found in the script. 

You may use your own word processor to write a script as long as you 

save the file in a text-only format. 

Statements may be entered in upper- or lower-case. 

A line in a script is limited to 80 characters. However, STN commands 

can be up to 256 characters in length. To continue a statement on the 

next line, put a backslash, \, at the end of each line that is continued on 

the next line. A single script statement can be 140 characters long. 

Scripts do not require an exact format style as you type in the statements. 

However, each statement MUST be entered on a new line. It is 

recommended that you use the style that is shown throughout this 

appendix. 

Follow the steps below to begin writing a script. More advanced script 

examples are included after this section. 

To ensure that all STN Express features are available while you are online, 

use the STNLOGON script instead of writing your own commands to logon 

to STN. 

Open a new script file by selecting New from the File menu within the 

STNEdit window. A new, untitled window is displayed.


Script 

Language 

Components 

The STN Express with Discover! Script Language is a miniature 

computer programming language. As such, it has many of the same 

components as other programming languages. The components of the 

Script Language include: 

• Variables - Temporary storage places for data, or places to 

store data that can change 

• Character Strings and Numbers – Constant, literal text and 

numeric data 

• File names - Names of transcript or data files on your PC 

• Labels - Identifiers for statements 

• Statements - Instructions to STN Express with Discover! that 

perform an action. For example, the SEND statement instructs 

STN Express with Discover! to send a string of characters to an 

online host or communications device. 

• Operators and Conditions – Elements that manipulate and 

compare pieces of data 

• Syntax requirements - Rules for organizing scripts and typing 

statements 

Variables 

A variable is a name for a place to store information. Specifically, a 

variable can store a number, a string of characters, a file name, or the 

result of a search. Use a variable when a specific value is unknown or 

will change within a script. For example, if you write a script that 

performs an author search, make the script flexible by using a variable 

for the author’s name instead of typing the author’s name in the script. 

Variables are named with an underscore followed by one to twelve 

alphanumeric characters. They are considered “declared” after their 

first use. Once a variable is declared, the same name may not be used 

to refer to another variable. 

Variables are always considered to be of type string (text), except for 

variables that represent search results (L-numbers). Variables are 

automatically converted to numbers (integers) when necessary for 

arithmetic operations or conditions. Attempts to perform arithmetic 

operations on non-numeric text result in errors when the script is run. 

To give a variable a value, use an assignment statement, described 

below, or the \> operator, described at the => statement. See also the # 

operator, explained under the => statement. 

Up to 200 variables are permitted within a script. If there are more 

variables, this is noted when you run the script online rather than when 

you use Check Command File. 

Variable values may not exceed 255 characters in length.


Character Strings 

Textual data is enclosed in double quotes and can be a string up to 140 

characters long. 

You may continue a string on a new line by typing a backslash, \, at the 

end of the line. 

To use the value of a string variable, type the variable along with the text. 

Place double quotes around the entire string. 

For example: 

_s = ”how to use” 

ECHO ”This is _s a variable in a string.” 

displays: 

This is how to use a variable in a string. 

Variables within strings are replaced by their values, converting integers to 

text. The # operator, along with a variable, is replaced by the number of 

answers in the answer set and is converted to text. 

If you want a variable within a string to be immediately followed by nonblank 

text, separate the variable name and text with a period. 

For example, 

_variable = ”con” 

ECHO ”This example string includes 

_variable.catenated text” 

displays: 

This example string includes concatenated text 

Special characters and escape characters within strings include: 

[CR] 

[TAB] 

[BS] 

[ESC] 

[BELL] 

[CTRL-A]...[CTRL-Z] 

[FF] 

Carriage return 

Move to next tab position 

Backspace 

Escape 

Sound bell (beep) 

Unprintable control characters 

Formfeed 

Note that many networks and STN Express with Discover! use control 

characters in normal operations. As a result, indiscriminate use of control 

characters may result in lost data, locked sessions, or terminated 

processes.


The characters, _, \, ”, [, and #, have special use within the script 

language and must be doubled if they are to be used within a string. 

In other words, to include a [ in a string, use two in a row: 

ECHO ”Here is a string with a left bracket\ 

(i.e., [[) in it.” 

displays 

Here is a string with a left bracket (i.e., [) in it. 

A distinction between upper- and lower-case is made when the 

characters are within a string and the number of spaces between words 

and letters is not ignored. 

Numbers 

The Script Language supports integers; there are no decimals or 

fractions. Type whole numbers in an ordinary way. For example 

_var = 42 

IF _var < 100 THEN 

To use a negative number, subtract a positive number from zero: 

_neg = -1 \* not allowed 

_neg = 0 – 1 

IF _neg < 0 THEN 

File Names 

Enclose file names within angle brackets, < >. All characters within the 

brackets are taken literally, but underscore characters are not allowed. 

File names may be included with variables. 

For example, 

CAPTURE ON \* a literal file name 

_var = \* assign a file name 

\* to a variable 

EXEC _var \* execute a script 

\* whose name is in _var 

CAPTURE OFF 

Labels 

A label or statement label identifies a line in a script so that other 

statements can refer to that line. Labels are named similarly to variables 

except that they begin with the @ character. The following are examples 

of valid labels: 

@start 

@error 

Refer to the CONTINUE, GOTO, GOSUB statements for examples of how 

to use labels.


Statements 

and Control 

Constructs 

The Script Language is composed of keywords and values. Keywords 

are words that have special meaning in the Script Language. Values are 

pieces of data in the form of variables, strings, numbers, or file names. A 

statement has at least one keyword, and some statements have 

parameters. A parameter is the object of the statement and may be a 

keyword, a value or a combination of keywords and values. You can 

sometimes think of statements as having verbs and objects. For example, 

in the statement GET _author, GET is the verb and _author is the object 

(parameter). 

The conventions used to describe the STN Express with Discover! Script 

Language are: 

1. Keywords are shown in upper-case letters, e.g., EXIT. 

2. Strings are shown in lower-case letters inside double quotation 

marks. For example, in the statement SEND ”string”, SEND is a 

keyword, and string is a string value. You may use a variable 

wherever you can use a string. 

3. Variables are shown in lower-case letters with a preceding 

underscore. For example, in GET _var1, GET is a keyword, and 

_var1 represents the name of a variable. 

4. Numbers are denoted by lower case letters or words. For example, in 

the statement PAUSE n n represents a number. 

3. Optional parameters are shown inside square brackets. For example, 

PAUSE n [SECONDS] means the PAUSE statement has a required 

parameter n, and an optional keyword, SECONDS. Do not type the 

brackets when you type the parameter or keyword. 

4. When there is a choice of parameters or values, the choice are 

enclosed in braces, and a vertical bar separates the choices. For 

example, in the statement CAPTURE {ON | OFF}, the keyword ON or 

the keyword OFF follows the CAPTURE keyword. 

5. File names are shown within angle brackets, DELETE . 

You may use a variable whose value is a file name wherever you can 

use a file name. 

7. Comments are preceded by \* and continue through the ends of their 

lines. The script processor ignores comments. 

The statements in the STN Express with Discover! Script Language are 

listed in alphabetical order.


Make sure you review the common statements, i.e., SEND, WAIT, =>, :, 

ECHO, IF, GOTO, and EXIT. 

=> 

: 

=> [host-command] [\!] [\> _var] (primary prompt statement) 

: [STN-reply] [\!] [\> _var] (STN secondary prompt statement) 

The => and : statements are shortcuts for a WAIT/SEND combination. 

The => command waits for a primary or level 1 prompt, “=>” on STN. 

The : command waits for a secondary or level 2 prompt, “:” on STN. For 

example, 

=> del history \* Send a delete history 

\* command 

: y \* and reply to the secondary 

\* prompt. 

is equivalent to 

SEND ”” \* Cause an arrow prompt. 

WAIT 

FOR ”=>” \* Wait for the arrow prompt 

SEND ”del history” \* and send a delete command. 

WAIT 

FOR ”:” \* Wait for the confirmation 

\* question 

SEND ”y” \* and reply. 

In each case, STN Express waits to receive a command prompt from 

STN. After receiving the arrow prompt, STN Express sends a delete 

history command and then waits for a secondary prompt from STN. 

STN responds with “DELETE ALL L# ITEMS? (Y)/N:” which STN 

Express recognizes as a level 2 prompt 

The => command works for online hosts other than STN. The : command 

is for STN only. 

Use the \! option if you want to edit the host command before it is sent 

(see also the EDIT statement). 

Use the \> operator to assign the L-number result of the command to a 

variable. For example, suppose the search command in the following 

statement produces L2 and 1492 answers: 

=> s acid cow \> _lnum 

The value of _lnum will be “L2”. Furthermore, the # operator can be used 

with _lnum to retrieve the number of answers in an L-number. The 

statement 

ECHO ”_lnum contains #_lnum answers.” 

displays 

L2 contains 1492 answers.


Assignment 

Statement 

_var = expression 

Use an assignment statement to assign a value to a variable. First type the 

name of the variable, then an equal sign (assignment operator), and an 

expression. An expression can be a variable, a string, a number, a file 

name, an arithmetic expression, or a function. For example 

_count = 0 

_count = _count + 1 

_author = ”dittmar, p” 

_filename = 

BEGIN/END 

BEGIN/END 

BEGIN/END forms a block of statements that are treated as a group. 

A BEGIN/END block usually follows an IF or ONEXIT statement. 

To use this statement, type BEGIN before the statements you want 

grouped together. Type END after the statement group. 

For example, 

IF (_status = ”NOT CONNECTED”) 

BEGIN 

ECHO ”DIALING...” 

SEND ”ATDT 555-5555” 

WAIT 

FOR ”CONNECT” CONTINUE 

FOR 5 SECONDS EXIT 

ECHO ”CONNECTED!” 

END 

This example executes every line between BEGIN and END only if the 

value of _status is “NOT CONNECTED”. Otherwise, the script continues 

after the END statement. 

BREAK 

BREAK [n [MILSEC[S]]] 

The BREAK statement sends a break to the host system. Enter the 

number, n, as either a variable or an integer. If x is not entered, 750 is the 

assumed value. 

For example, 

BREAK 500 

sends a break 500 milliseconds in duration.


CAPTURE 

CAPTURE {ON | OFF} 

The CAPTURE statement turns on or off the capturing of your online 

session. /A opens the file name in append mode. 

Entering a file name is optional. If you do not enter a file name, you 

must still type . Typing CAPTURE ON prompts you to enter the 

transcript file name. 

Typing CAPTURE OFF assumes that you want the currently opened 

transcript file closed. 

For example, 

CAPTURE ON 

ECHO ”THIS LINE OF TEXT” 

CAPTURE OFF 

results in the line “This LINE OF TEXT” being placed in a file named 

tranfile in the Transcripts folder defined in your General Preferences. 

If the file exists, you may opt to append the file by clicking Append. 

Click the Save button to replace the file. 

Once the file is open, the output from your session up to the CAPTURE 

OFF statement, is placed in the transcript file. Capturing is turned off 

when STN Express with Discover! receives the CAPTURE OFF 

statement. 

If an error occurs, the _$filerror system variable is non-zero. 

CLOSE 

CLOSE 

The CLOSE statement closes the currently open file. 

For example, 

CLOSE 

closes the data file that was opened by the OPEN statement. 

If an error occurs at the end of the file, the _$filerror system variable is 

non-zero.


CONTINUE 

CONTINUE 

The CONTINUE statement is used to continue processing a script beyond 

the current SEND, WAIT FOR, and TRYAGAIN statements. 

For example, 

SEND ”X” 

WAIT 

FOR ”LOGINID” CONTINUE 

FOR 20 SECONDS GOTO @ERR 

SEND _loginid 

If “LOGINID” is received from the host, the script continues at the SEND 

statement. 

DELETE 

DELETE 

The DELETE statement deletes a specific file. 

For example, 

_filename = 

DELETE _filename 

deletes the file named OLDFILE.txt. 


DROP DTR 

DROP DTR 

The DROP DTR statement is used to set the DTR (Data Terminal Ready) 

circuit to an “off” state. In some rare situations, you may need to control 

the DTR setting on your modem. See also RAISE DTR. 

ECHO 

ECHO “string” [NOCR] 

The ECHO statement is used to display a character string or variable on 

the screen. The “string” can be zero or more characters, variables, or 

both. 

For example, 

_var = ”example” 

_item = ”ECHO statement.” 

ECHO ”This is an _var of the ” NOCR 

ECHO _item 

displays “This is an example of the ECHO statement” on your screen. 

A carriage return automatically occurs after this statement. To suppress it, 

use the NOCR keyword.


When you use the ECHO statement in conjunction with the GET 

statement, echo a blank line first (carriage return only). Then ECHO a 

prompt or message. 

For example, 

ECHO ”” \*outputs a blank line to the screen 

ECHO ”Enter your Password:” 

GET _password HIDDEN 

EDIT 

EDIT {ON | OFF} 

The EDIT statement is used to interact with the script processor by 

pausing the script after each line is sent and displaying a text editing box 

that allows you to modify the next line before it is processed. The 

changes made in the text editing box are not saved in the script file. The 

default is EDIT OFF. 

For example, 

=> FILE CAPLUS \* This line is sent as typed 

EDIT ON 

=> S ASPIRIN \* This line can be modified 

\* before it is sent 

EDIT OFF 

=> D 1-3 ALL \* This line is sent as-is 

You may use \! as a shortcut for the EDIT statement. Use \! on the => 

and : statement lines for STN scripts. This shortcut must occur at the 

end of a line. 

EXEC 

EXEC 

The EXEC statement is used to execute another script from within a 

script. The script file name is required. 

Scripts may be executed eight levels deep. Variables defined in the 

calling script are also available for the called script. When the called 

script completes, processing continues on the line immediately after the 

EXEC statement in the calling script. 

For example, 

_filevar = 

EXEC _filevar 

ECHO ”_filevar has completed processing.” 

executes the script SECOND SCRIPT. Then it returns to the calling 

script and prints: 

SECOND SCRIPT has completed processing.


All scripts that are executed must reside in the User Scripts or 

Predefined Scripts folder as defined in General Preferences (located in 

the Setup menu on the Main Menu bar). The User Scripts folder is 

checked first for the script. If it is not found, the Predefined Scripts folder 

is checked. If the script is not found in either folder, an error message is 

displayed. If an error occurs, the _$filerror system variable is non-zero. 

EXISTS 

EXISTS 

The EXISTS statement tests for the existence of a file, first in the User 

Scripts and then in the Scripts folder. It sets _$filerror to zero of the file 

exists and to a nonzero value if the file does not exist. 

EXIT 

EXIT 

The EXIT statement defines a point to leave the script. 

EXIT has no parameters. An exit is assumed after the last statement in a 

script. Thus, an EXIT statement is not required in any script. More than 

one EXIT statement may be used in a script. If an ONEXIT statement 

exists in a script, the ONEXIT block is executed before exiting. If the 

ONEXIT statement includes an EXIT statement, an exit occurs immediately 

when that exit is executed. 

GET 

GET _varname [HIDDEN] 

The GET statement is used to accept input from the keyboard to use in a 

script. 

When a GET statement is reached in the script, processing is transferred 

to the user. A text entry box is displayed in which the user may type a 

line. Typed items, up to but not including the first carriage return, are 

placed in _varname. The script then continues at the next statement. 

All input lines are scanned for a colon (:). If found, GET returns only the 

characters that follow the colon. 

If the HIDDEN option is present, the typed characters are not displayed 

on the screen. 

For example, 

ECHO ”Please enter your password:” 

GET _passwd HIDDEN 

prompts you for your password. When your password is entered, it is 

processed but not displayed.


GOSUB 

GOSUB @LABEL 

The GOSUB statement is used to branch to a different location in the 

script with the option of returning to the statement after GOSUB. 

This statement is useful when an identical set of statements is executed 

from various points in the script. 

GOSUB has only one parameter, a label of a set of statements that may 

reside outside of the normal flow of the script. When GOSUB is 

reached, processing moves to the indicated label and continues 

processing until a RETURN statement is reached. The RETURN 

statement causes processing to continue with the statement following the 

GOSUB statement. 

GOSUBs may be nested up to eight levels. 

For example, 

ECHO ”Right before the GOSUB.” 

GOSUB @SUBROUTINE 

ECHO ”Right after the GOSUB.” 

EXIT 

@SUBROUTINE 

ECHO ”Within the GOSUB.” 

RETURN 

displays 

Right before the GOSUB. 

Within the GOSUB. 

Right after the GOSUB. 

GOTO 

GOTO @LABEL 

The GOTO statement is used to continue processing at a line that is not 

directly after the current line of a script. This statement is useful to 

redirect processing. 

GOTO is similar to GOSUB except that there is no option to RETURN 

unless it is initiated with another GOTO. 

For example, 

IF (_var1 = ”FIRST”) GOTO @LABEL1 

ECHO ”Value of var1 is not FIRST.” 

EXIT 

@LABEL1 

ECHO ”Value of var1 is FIRST” 

EXIT 

outputs only one of the above ECHOed lines before exiting depending on 

the value of _var1.


IF 

IF (condition) block [ELSE block] 

The IF statement is used to execute one or more statements based on a 

certain condition. Conditions are defined later in this Appendix. 

The IF/ELSE statement forms a construct that decides which statement to 

execute next. If the condition is true, the statements directly following the 

IF are executed. If the condition is false, the statements directly following 

the ELSE are executed. 

For example, 

IF (_phoneno = ””) 

BEGIN 

ECHO ”Enter phone number:” 

GET _phoneno 

END 

ELSE 

echo ”Dialing...” 

\* if no telephone number was 

\* given 

\* else phone number exists 

SEND ”ATDT _phoneno” 

\* single statement as a block 

Note that the SEND statement is outside of the IF/ELSE construct. It is 

executed regardless of the condition. 

ONEXIT 

ONEXIT block 

ONEXIT is used to specify a set of statements to execute before leaving a 

script. 

The ONEXIT statement may be placed anywhere within a script. It cannot 

contain a GOTO or RETURN statement. An EXIT statement within an 

ONEXIT block signifies an EXIT when the EXIT statement is reached. 

Statements following the EXIT statement in the ONEXIT block are ignored. 

The block portion of the statement may be entered as one line, or as a set 

of statements between BEGIN and END. 

For example, the statements 

ONEXIT 

BEGIN 

ECHO ”These two lines will always be” 

ECHO ”executed upon exiting the script.” 

END 

cause the two lines to be displayed to the screen when you leave the 

script.


OPEN 

OPEN [ {/R | /W} ] 

The OPEN statement is used to open a new or existing file from within a 

script. 

Entering the file names is optional. If no file name is supplied, you are 

prompted to enter one. The /R option opens the file to read only. The 

/W option allows both reading and writing in the file. The default option 

is /W. 

For example, 

_error = ”Command timed out. Error ##36.” 

DELETE 

OPEN 

WRITE _error 

CLOSE 

places the following message in a file named “ERROR FILE”: 

Command timed out. Error #36. 


PAGE 

PAGE 

The PAGE statement forces output to a new page when printing. 

PAGE is issued with no parameters and causes output from a captured 

file to begin at the start of a new page. The statement places a [CTRL]-L 

in the file. This is the control character sequence to start a new page. 

PAUSE 

PAUSE {n [SECOND[S]] | [UNTIL time]} 

The PAUSE is used to halt script processing for a specific time. 

Enter the number of seconds, n, as an integer or a value within a 

variable. If n equals zero, the pause is forever. 

The UNTIL time option allows you to specify a certain time of the day, 

using a 24-hour clock. 

For example, 

PAUSE 1 SECOND 

PAUSE UNTIL 14:45 

\* pause for 1 second 

\* pause until 2:45 pm 

PRINT 

PRINT {ON | OFF} 

Use the PRINT statement to turn “slave” printing on or off. Slave printing 

causes the transcript to be printed as the online session progresses. 

Slave printing is not recommended.


RAISE DTR 

RAISE DTR 

Use the RAISE DTR statement to set the DTR (Data Terminal Ready) 

circuit to an “on” state. See also DROP DTR. 

READ 

READ _varname 

The READ statement reads a single line from the OPEN file and stores the 

value, without a carriage return character, in _varname. 

For example, 

ECHO ”reading first line of INPUT FILE” 

OPEN 

READ _line 

CLOSE 

The cursor remains on the same line. The INPUT FILE is opened and the 

first line is read into the variable _line. 

If an error occurs, the _$filerror system variable will be non-zero. 

RETURN 

RETURN 

The RETURN statement is used to return the script processing to a saved 

point in your script. This is usually after a GOSUB statement. 

For example, 

GOSUB @SUBROUTINE 

ECHO ”processing will return to this point.” 

EXIT 

@SUBROUTINE 

ECHO ”After printing this line...” 

RETURN 

displays the following: 

After printing this line... 

processing will return to this point. 

SEND 

SEND ”string” [EDIT] [HIDDEN] [NOCR] 

The SEND statement is used to send a string to the online host. 

(Technically, the string is sent to the communication port specified in the 

logon setup. Therefore, for example, a string can be sent to a modem 

before STN Express is connected to the host.) 

The “string” and other parameters may occur in any order after the SEND 

statement. The “=>” and “:” statements are specific forms of the SEND 

statement that are described earlier in this section.


EDIT is an option that allows the string to be edited before it is sent. 

EDIT works as \! does in the => and : statements. 

HIDDEN does not display the string as it is sent. This is useful when 

sending passwords. 

A carriage return is automatically included after the string. To suppress 

it, use the NOCR keyword. 

For example, 

SEND ”+++” NOCR 

SEND ”ATDT 555-1212” 

sends: 

+++ATDT 555-1212 

to the modem. 

STNLOGON 

STNLOGON 

The STNLOGON statement is used to execute the STNLOGON script that 

logs you on to STN International. STNLOGON assumes that there is 

already a connection to STN. Specifically, STNLOGON sends a carriage 

return and expects the reply to be “Welcome to STN International! Enter 

x:” message is displayed.) 

SUBSTR 

SUBSTR (_var, begin, length) 

SUBSTR is more of a function than a statement. SUBSTR takes a string 

of characters and finds a substring. This statement takes on the value of 

a string. The value is a portion of the string _var. It begins with 

character number begin and continues for a length characters. “begin” 

and “length” must be numeric constants. 

For example the statements 

_var1 = ”xxx remove this portion xxx” 

_var2 = SUBSTR(_var1,5,19) 

ECHO _var2 

display the following contents of _var2: 

remove this portion 

SUBSTR may be used in conditions. For example, 

IF (SUBSTR(_var1,1,3) = ”xxx”) GOTO @label


TRYAGAIN 

TRYAGAIN n [TIMES] [ [THEN] block] 

The TRYAGAIN statement is used to repeat the previous SEND statement 

a specified number of times. 

This statement works only in the context of the WAIT-SEND statement pair. 

It repeats the previous SEND up to n times. After the nth attempt, 

processing either performs the THEN block or EXITs. 

For example, 

SEND ”ATDT 555-1212” 

WAIT 

FOR ”CONNECT” CONTINUE 

FOR ”NO CARRIER” EXIT 

FOR 5 SECONDS TRYAGAIN 5 TIMES THEN GOTO @LABEL 

This sends the phone number and waits 5 seconds for either CONNECT 

or NO CARRIER. If the response is not received, the phone number is 

sent up to four more times. If the response is still not received, the 

process jumps to the @LABEL label. 

UPLOAD 

UPLOAD [LNUM _var1,_var2,_var3...] 

The UPLOAD statement is used to upload a structure query to STN. The 

result of the UPLOAD on STN is one or more L-numbered queries. 

The LNUM keyword indicates the beginning of a list of variables. The 

variables are assigned the L-number or L-numbers of the uploaded 

structure. Usually, only one variable is needed. Multiple variables are 

needed when a reaction query with multiple participants is uploaded in an 

STN file that does not support reaction searching. In that situation, each of 

the participants is uploaded into its own L-numbered query. Commas must 

separate variables in the list. 

For example: 

UPLOAD LNUM _line1 

This statement uploads the structure query file STR1.STR to STN and 

store the resulting L-number value in the _line1 variable. 

The file name to upload should be preceded by a space. It is the name of 

a chemical structure file created Structure Drawing. 

If an error occurs, the _$filerror system variable is non-zero.


USER 

USER 

The USER statement is used to temporarily halt script processing. 

Control is turned over to the user. This statement lets you place specific 

breaks in a script where you want to take control of the online session. 

Control is returned to the script when you press the END key. 

VT320 

VT320 {ON | OFF} 

The VT320 statement is used to turn ON or OFF VT320 terminal 

emulation and is useful when you connect to STN via a VAX with a menu 

system and when you connect to an online host that offers a menu 

system. 

WAIT 

WAIT [_var1] [LNUM _var2] for-list 

The WAIT statement is used to pause script processing until a specific 

response is received from the online host. This statement results in data 

being read from the incoming communication port one line at a time. A 

line includes everything up to a carriage return. 

_var1 contains the last line received from the host. 

LNUM _var2 puts an L-number into the variable _var2. 

for-list is one or more: 

FOR FORcond [THEN] block 

This is defined as: “If the FORcond is met, then execute these 

statements.” 

The block is optional, except for the last FORcondition. Often the block 

contains a CONTINUE statement. 

For example, FORcond is either: 

“string” 

(substring received from host) 

or: 

n [SECOND[S]] (passing of time, n, can be an integer or a 

variable) 

If n is zero, the WAIT is forever. 

WRITE 

WRITE ”string” [NOCR] 

The WRITE statement is writes a line of text in the currently open file. 

WRITE places the “string” in the open file, followed by a carriage return. 

If NOCR is present, the carriage return is suppressed. Lines are always 

written to the end of the file. To erase the contents of the file before 

writing to it, use the DELETE statement. 

If an error occurs, the _$filerror system variable is non-zero.


Operators and 

Conditions 

Operators and conditions are components of statements. Arithmetic 

operators manipulate the values of numbers. String operators work on text 

strings. Conditional operators compare the values of strings and numbers 

in IF statements. Special operators are used in specific situations. 

Arithmetic 

Operators 

Use the arithmetic operators in assignment statements to perform 

arithmetic on numbers. The arithmetic operators do not function inside 

strings or conditions. 

+ addition add two numbers together 

- subtraction subtract one number from another 

* multiplication multiply two numbers 

/ division divide one number by another 

String Operators 

+ concatenation join two strings (not inside double quotation 

marks) 

. concatenation denote the end of a variable name inside double 

quotes 

Conditional 

Operators 

To control execution of a statement or a set of statements based on the 

value of a variable, use an IF statement with a condition. 

Numbers and strings 

= equality numbers or strings are equal 

inequality numbers or strings are not equal 

Numbers 

> greater than 

< less than 

>= greater than or equal to 


Examples 

_s = ”string” 

IF _s = ”string” 

IF _s = ”string ” 

IF _s = ”STRING” 

IF _s INCL ”ring” 

IF _s NOTINCL ”cow” 

_var1 = 10 

_var2 = 5 + 5 

IF _var2 = _var1 

IF _var2 var1 

IF _var1 > 0 

IF _var2 < 4 

IF _var1 >= 10 

IF _var1 statement). 

\> L-number Assign the result of a command to a variable 

(=> statement). 

# answer count Retrieve the number of answers from an 

L-number variable.


Other Script 

Examples 

Use these scripts as models for scripts that meet your needs. To see other 

scripts, look in the Scripts and PSSfiles folders in your STN Express 

installation. 

Registry Number 

Script Example 

Recall the script shown at the beginning of this appendix: 

\* Display CAS RNs in the Registry file on STN. 


=> DIS 50-00-0 

=> DIS 7777-77-7 

=> LOG Y 

It does its job but is not very flexible. For example, what if you have long 

list of CAS Registry numbers instead of just a few? Use the OPEN, READ, 

IF, and CLOSE statements to process a file of Registry Numbers. 

\* STN Express script to read list of RNs from a file 

\* and display information for each Registry Number. 

\* Open the data file for reading. There is one RN on 

\* each line. 

OPEN /R 

=> file registry 

\* Process all the RNs in the file 

@readloop 

\* Read an RN from the data file. 

READ _rn 

\* If an RN was read, send a DISPLAY command to STN. 

IF (_$filerror = 0) 

BEGIN 

\* Display the requested substance 

=> dis _rn 

GOTO @readloop 

END 

\* Close the input file 

CLOSE 

=> 

EXIT


Author Search 

Script Example 

ECHO ”” 

ECHO ”This is a script for running author searches.” 

ECHO ”Press [Esc] at any time if you would like to\ 

stop.” 

ECHO ”” 

ECHO ”In the pop-up box, enter the last or family\ 

name of the author:” 

GET _lastname 

ECHO ”In the pop-up box, enter first or given name\ 

or initial:” 

GET _firstname 

\* Use the STN expand command to provide choices of 

\* names. 

=> 

=> expand _lastname _firstname/au 

ECHO ”Enter the e-numbers to search, e.g., e3-e5 or\ 

e3,e7) or end” 

GET _enums 

IF (_enums = ”end”) 

BEGIN 

ECHO ”Ending author search at your request.” 

=> 

EXIT 

END 

=> 

=> search _enums \> _results 

\* If the search yielded zero answers, there is 

\* nothing to display. Inform the user and exit. 

IF (#_results = 0) 

BEGIN 

ECHO ”There are no answers for your query.” 

=> 

EXIT 

END


\* The search found hits, so ask how many should be 

\* displayed. 

ECHO ”How many answers would you like to display? 

(e.g., \#_results or 0):” 

GET _display 

IF (_display > 0) 

BEGIN 

ECHO ”Please provide a transcript name to use to\ 

save your answers.” 

CAPTURE ON 

\* Don’t try to display more answers than are 

\* available. 

IF (_display > #_results) THEN _display = 

#_results 

=> 

=> dis 1-_display bib 

CAPTURE OFF 

END 

ECHO ”Your author search is now complete.” 

=> 

EXIT


Helpful Hints 

As you begin writing scripts, you may want to keep the following hints in 

mind. 

• Check Command File checks your script for some errors. 

Getting an error-free script from the command file checker does 

not guarantee that the script will do what it was intended to do. A 

clean bill of health from the command file checker also does not 

guarantee there are no errors in the script because some errors 

cannot be found until the script is run. 

• You may create a script in any word processor or text editor that 

allows you to save a file as plain text. 

• Add comments to a script by placing a \* anywhere on the line. 

To display a comment on the screen, use the ECHO statement. 

• Comments help make your script more readable or 

understandable to others. 

• The keywords in the STN Express with Discover! script 

language are not case sensitive. However, upper and lower 

case do matter in strings, and spaces count, too. For example, 

“Yes” is different from “yes”, and “STN Express” is different 

from “STN Express”. 

• Use a standard spacing and indentation scheme to make your 

scripts more readable. 

• Enclose strings in the SEND, WAIT, FOR, and ECHO statements 

in double quotes. 

• Use the Escape or Clear key to stop a script from processing 

• Place a \ at the end of a line to continue a statement or string on 

the next line 

• All STN Express with Discover scripts must be in either the User 

Scripts folder or the Predefined Scripts folder. When looking 

for a script to execute, STN Express with Discover! first checks 

the User Scripts folder, then the Predefined Scripts folder. 

• Εnter only the unique portion of the prompt when using the 

WAIT FOR statement. 

• Use the SEND, WAIT FOR, and TRYAGAIN statements together 

because TRYAGAIN will resend the last item that was sent using 

a SEND statement. Many times, TRYAGAIN is an optional part 

of the statement trio because you would not want to resend 

some items, e.g., login ID or password.


Logon Scripts 

There are two separate steps to logging on to an online host: 

1. connecting to the host through a telecommunications network 

2. logging on to the host 

STN Express includes support for several telecommunications networks 

and online hosts. Before you take the time to write your own connection or 

logon script, find out whether STN Express already provides the scripts 

you need. Also, you may find it easier to use the Watchme feature than to 

write your own logon script. Refer to Chapter 3, Logon Setup for STN, for 

details about Watchme. 

Predefined Setup 

Variables 

If you intend to write your own scripts that connect through a network or 

log on to an online host, be sure you understand the details of a logon 

setup. Many of the values defined in a logon setup are available to STN 

Express with Discover! scripts as variables. Below is a list of these 

variables, organized by the area within Setup that sets the value. 

Setup Definition Dialog Box 

• Host Information area 

_$logid –Value of Login ID (for host) 

_$password – Value of Password for host 

_$service – Value of Host Name; set to “STN” for all STN hosts 

_$stncenter – Name of STN Node (Columbus, Karlsruhe, or 

Tokyo) 

• Path Information area 

_$connvia – Value of Connect via 

• Logon Method 

_$network – Value selected from network list 

• Network Logon area 

_$nua – Value of NUA (Network User Address) 

_$nui – Value of NUI (Network User Identifier) 

_$nup – Value of NUP (Network User Password) 

• Communication Settings area 

_$baud – Value of Speed 

_$dialtype – Value of Dial 

_$phoneno – Value of Primary Phone # 

_$phoneno2 – Value of Secondary Phone # 

• Host Settings tab 

_$qservname – Value of Choice of service (Questel) 

_$graphics – Value of Graphics (STN) 

_$stnport – Value of STN Port (STN) 

_$modinit – Value of Modem Configuration - Initialization String


Advanced Dialog Box 

− 

− 

− 

− 

− 

− 

_$gwcomm1 through _$gwcomm5 – Value of Execute at 

command prompt fields one through five 

_$gwloginp – Value of Prompt Character strings - Login 

_$gwcommp – Value of Prompt Character strings - Command 

_$gwpassp – Value of Prompt Character strings - Password 

_$gwid – Value of Gateway Login ID 

_$gwpw – Value of Gateway Password

Appendix 

D 

Questel 

Features 

on STN 

Questel 

The following features are available while accessing Questel on STN 

Express with Discover!. 

Questel D–1 

• Offline Structure Building - build a structure query offline to 

search Questel’s Generic DARC system. Use the STN Express 

with Discover! structure drawing tools and palettes described in 

Chapter 6, Structure Queries, to build your structure. 

• Autologon - create a logon setup to automatically log on to 

Questel 

• Upload Structure Query - upload structures drawn on STN 

Express with Discover! to search files on Questel’s Generic 

DARC system 

• Capture Online Displays - capture text and graphics results from 

an online session to a transcript. You may browse, print, edit, or 

export your transcript. 

Structure 

Query 

Building 


Prepare Query button if it is located on your Structure Drawing Toolbar. 

A new Untitled “Standard” structure drawing window is displayed. 

Select New/Questel from the File menu or click the button representing a 

new Questel structure query if it is located on your toolbar. See Chapter 

6, Structure Queries, for details about adding buttons to the Structure 

Drawing Toolbar. 

Draw your Questel structure query using the STN Express with Discover! 

Structure Drawing menus, tools, and palettes. Refer to Chapter 6, 

Structure Queries, for details. 

Converting 

Existing STN 

Structures 

to Questel 

Structures 

Select Open from the File menu to display the Open Query dialog box. 

Select a query to open by highlighting its name in the scrollable File Name 

list. The structure is previewed to the right of this list. 

Then click the radio button next to Questel. The structure is converted to a 

Questel structure format in the preview box.

D–2 Questel 

Click OK. The structure is placed in an Untitled Questel structure drawing 

window. The original structure query is not changed. 

Because structure drawing features may differ for Questel, it is 

recommended that you check the structure attributes by selecting Query 

Verification from the QueryDef menu. This should be done before you 

save and upload the query. 

For example, during conversion from STN to Questel, ring isolation 

settings are ignored, bond settings are reinterpreted using the Questel 

bond algorithm, and other attributes are ignored. Differences also occur 

in the shortcuts and variables available on Questel. Unrecognized nodes 

are converted to A (Any Atom) settings. 

Query Verification 

STN Express with Discover! verifies structure building according to an 

algorithm that corresponds to Questel’s use of aromatic, tautomeric, and 

exact settings. For example, bonds in even-numbered cyclic pathways 

with alternating single and double bonds are set as aromatic bonds. 

Bonds in tautomeric structures are marked as tautomeric.

Questel D–3 

Free Sites 

Free sites are used to specify the degree of substitution allowed at a 

specified position. 

To insert a free site, select one or more nodes using the Selection tool. 

Then select Free Sites from the QueryDef menu. The Free Sites dialog 

box is displayed. Click the number of free sites for the nodes you 

selected from the scrollable list. Then click OK. 

The number you selected represents the maximum number of attachments 

at that node. Because free sites are a maximum, the retrieval includes all 

lower degrees of substitution as well. 

☞ Bond types are not considered, e.g., an atom attached by a double 

bond is considered a single attachment. 

If no free sites are specified, the system completes the normal valency of 

the atoms with hydrogens when executing the search. 

Autologon 

For information on creating an automatic logon to Questel, refer to 

Chapter 5, Using non-STN Hosts and Appendix C, Script Language. 

As with STN, storing your logon ID and password are optional. If you do 

not enter them in your setup, you are prompted for them at logon. To 

logon to Generic DARC, set the “choice of service” in the Host Settings 

tab of your Setup to G. 

Always set the Host Name in your setup to Questel. 

After logging on to Generic DARC, you can run the Command file 

“qst_op.sc” to set the language and the terminal type. The terminal type is 

set to S for STN Express with Discover! support.

D–4 Questel 

Uploading 

Structure Queries 

Select Exit Structure Drawing from the File menu to search a structure 

query on Questel’s Generic DARC system. You are prompted to save and 

name your structure query. 

Click the Logon menu from the STN Express Main Menu bar or click the 

Logon button if it is located on the Main Menu Toolbar. Choose to logon 

to your Questel setup. The Capture Session dialog box is displayed. 

If you are prompted to enter a transcript name to save your online 

session, i.e., text and graphics, type a name in the File Name text box and 

click Open. 

After you connect to Questel, select Upload Structure Query from the 

Query menu. Select a structure query to upload and click Open. 

Switching 

from Generic 

DARC to 

Questel 

You may switch from Generic DARC to the Questel system while online by 

using the BI option. If you experience problems, log off and then log back 

on to Questel.

Appendix 

E 

MDL Molfile 

Conversion Assumptions 

STN Express fi MDL Molfile 

exact 

exact/normalized 

normalized 

unspecified 

ring/chain 

chain 

ring 

manually set 

set by STN Express 

stereo 

G-groups 

shortcuts 

ring, ring/chain, chain 

variables 

X 

M,Q 

Id 

all others 

Nodes Nodes 

Attributes 

Reaction centers 

CC 

PC 

XC 

NC 

NON 

reactant, reactant/reagent, reagent 

product 

delocalized charge, match level, element count, 

variable points of attachment, stereo centers and bonds, and generic 

definitions 

connectivity 

ring bond counts of 2, 3, or 4 

all other ring counts 

all other Non-H connections 

repeating units 

single node 

all others 

Bonds 

exact 

any 

any 

any 

ring/chain 

chain 

ring 

ring/chain 

single 

lists or R-groups 

superatoms 

ignored 

halogen list 

Q 

* 

A 

make/break 

change 

center 

not center 

none 

reactant 

product 

ignored 

translated 

ignored 

translated to substitution 

counts 

translated 

ignored 

H count H ct. (>4 fi ‡4) 

isotope, valency and charge 

translated 

ring isolation assigns ring bond count of *

E–2 MDL Molfile Conversion Assumptions 

MDL Molfile fi STN Express 

MDL Molfile fi STN Express 

Bonds 

single 

single exact 

double 

double exact 

aromatic 

single normalized 

S/D 

unspecified 

S/aromatic 

single exact/normalized 

D/aromatic 

double 

exact/normalized 

any 

unspecified 

ring 

ring 

ring/chain 

ring/chain 

chain 

chain 

stereo double 

double exact 

stereo single 

single exact 

reaction centers 

center 

make/break 

change 

make & change 

not center 

none 

XC 

CC 

PC 

CC 

NC 

NON 

Atoms Atoms 

list 

G-group 

R-group 

G-group 

* Id 

any unrecognized symbol 

A 

Attributes Attributes 

charge, valence, and isotope 

translated 

substitution count 

ring/chain connectivity 

ring bond count 

ring connectivity 

all bonds in a ring system are * 

repeating groups 

stereochemistry, unsaturated atom, exact change, and no implicit 

hydrogens 

ring isolated 

translated 

ignored

Appendix 

Connecting to a Host 

Through a Gateway 

Connecting to a Host F–1 

FOverview 

STN Express can connect to STN or another host directly over the 

Internet using the telnet protocol. Depending on your organization’s 

network or security requirements, there may be a telnet gateway, a 

firewall, or a proxy server (all referred to as a gateway) between your PC 

and the host computer. STN Express can connect through most gateways. 

If you can telnet to the host, STN Express will be able to connect to it. 

To connect through a telnet gateway, you must know the details of the 

gateway’s prompts and interaction. For example, if the gateway prompts 

for a loginid, you must know the characters in that prompt. You must also 

know the gateway command for completing the connection to the host. 

Because a gateway is specific to your organization, you may wish to 

consult your network administrator or computer support group about 

connecting to and logging on to your gateway. 

Example 

Suppose you want to connect to STN Columbus and have a telnet 

gateway that requires that you log into it and then type the destination host 

name or IP address. After you connect to the gateway, a transcript of the 

steps required to navigate through the gateway might look like the 

following. The gateway’s messages, which are not of interest to STN 

Express, are shown in a normal font, the gateway’s prompts are shown in 

a bold font, and the information you type is shown in italics. (For 

security, the password is not shown.) 

Welcome to HQ telnet gateway. 

User: asmith 

Password: 

User asmith OK 

Ready> stnc.cas.org 

STN Express can automatically navigate through the gateway if it is aware 

of the gateway’s login prompt (User:), password prompt (Password:), 

and command prompt (Ready>). You may use the STN Setup Wizard to 

provide this information to STN Express. If you want to connect to a host 

other than STN, or if you prefer not to use the Setup Wizard, create or 

modify your setup as described below.

F–2 Connecting to a Host 

Modifying 

Your Setup 

Follow these steps to modify your setup in order to connect to an online 

host through a telnet gateway: 

1. In the Setup Definition dialog box, type the name or address of the 

gateway in the Host Name or IP address box. This causes STN 

Express to connect to the gateway instead of directly to STN or 

another host. 

2. In the Setup Definition dialog box, click the Advanced button to open 

the Advanced dialog box. 

Advanced 

Dialog Box 

Values 

Prompt Character 

Strings 

The values that you enter for Prompt Character strings define the 

prompts sent by the gateway. You may ignore other messages the 

gateway might display. Your gateway might issue all or only some of the 

three prompts that STN Express supports. In general, leave the Prompt 

Character strings box empty if your gateway does not display a 

particular prompt. 

Login 

The login prompt specifies the way the gateway asks for your loginid or 

user name. For the example gateway, the prompt is User:.

Connecting to a Host F–3 

Password 

When a gateway asks for a password, it issues the password prompt. 

Password: is the example gateway’s password prompt. 

Command 

A gateway displays the command prompt when it is ready to accept the 

command that causes it to connect to the online host. In the example 

gateway, Ready> is the command prompt. 

Optional 

Type the responses to the loginid and password prompts Optional area. If 

you choose not to save your loginid or password, or both, in the logon 

setup, STN Express will ask for them when needed. 

Type your gateway loginid in the box. If you do not know your gateway 

loginid, contact your network administrator. In the example, the loginid is 

asmith. 

If you enter your gateway password, it is encrypted and saved with the 

logon setup in express.ini. The password is not visible when typed. 

If you save your password in the logon setup, STN Express asks you to 

retype the password after you click OK. 

Execute at 

Command Prompt 

After you have logged in to the gateway, the gateway may display a 

prompt that indicates it is ready to accept commands. Enter up to five 

gateway commands in the boxes. Typically only one command is needed, 

and this might be a telnet command, a connect command, or something 

similar. In the example, all that’s needed is the host name or IP address of 

the destination, stnc.cas.org. 

☞ You can find the names and addresses of the supported hosts in 

the Setup Definition dialog by selecting the online host in the 

Host Name list and looking at the Host Name or IP address 

box. 

Interaction 

with a 

Gateway 

STN Express communicates with a gateway as follows: 

• After matching the Login prompt, STN Express with Discover! 

sends the Gateway Login ID 

• After matching the Password prompt, STN Express with 

Discover! sends the Password 

• Each time the Command prompt is matched, STN Express with 

Discover! sends the value in the next Execute at command 

prompt field 

☞ Matching of control characters within a prompt is not supported.

F–4 Connecting to a Host 

Custom 

Logon Setup 

for STN 

Express 

Versions 

prior to 5.0 

Starting with STN Express 5.0, a custom logon procedure is not required 

to make use of the Advanced Gateway options. The Gateway.sc script will 

automatically run if any of the Prompt Character strings boxes are not 

empty. Older, custom logon setups for gateways can be used in STN 

Express 6.0, and the following information has been retained as 

documentation for them. 

Connecting to a host system through a gateway using a Custom Logon 

method requires several steps. Each step typically requires that an STN 

Express with Discover! script be included within the Custom Logon 

section. These steps include: 

1. Connecting to the gateway: 

• Identify a script to connect to the gateway. No script is needed for 

this step for a Winsock connection. 

• Add this script as the first script in the Custom Logon section. 

• Set the values of the Communication Settings section to allow 

connection to the gateway, not to the host system. 

2. Logging on to the gateway and issuing the command to connect to the 

host system: 

• Add Gateway.sc as the next (or first) script in the Custom Logon 

• Fill in values in the Gateway Configuration section in the 

Advanced dialog box to allow logging on to the gateway. 

• Enter the command used to connect from the gateway to the 

online host in the Execute at command prompt field, e.g., telnet 

stnc.cas.org. 

3. Logging on to the host system: 

• Add the script normally used to log on to the host system as the 

last script in the Custom Logon Script List. Always use 

STNLOGON to log on to STN. 

☞ 

If you have difficulties using the Gateway.sc script to connect 

through a gateway, consider using the Watch Me function, 

described in Chapters 3 and 5, as an alternative.

Appendix 

G 

Overview 

Network Installation 

Network Installation G–1 

The Setup program for STN Express with Discover! offers special features 

for shared, network installations. In general, creating a network 

installation of STN Express is a three-step process: 

1. Install STN Express on the server. 

2. Share the server installation (make it visibile on the network). 

3. Install STN Express on one or more client PCs. 

The result is a shared network folder that contains the STN Express 

programs and one or more client installations that refer to the shared 

folder. 

Features and 

limitations 

· STN Express with Discover! and its setup program support the 

Universal Naming Convention (UNC) standard, e.g., 

\\APPSRV\STNEXP and mapped network drive letters. 

· If you use mapped drive letters, be aware that the EXPRESS.INI file, 

stored on the client PC, contains paths to the STN Express installation 

on the server. Therefore, the network share that contains the STN 

Express with Discover! applications must always be mapped to the 

same client drive letter (the drive letter may be different on each 

client). 

· The server installation may be performed at the server or across the 

network. 

+ Review the ReadMe file on the CD-ROM disc for details pertaining to 

network installations before proceeding. Any last minute changes are 

documented there.

G–2 Network Installation 

Installing STN 

Express on a 

Server 

To install or upgrade the software on your server, run SETUP.EXE and 

choose the Network Server option from the Setup Type section of the 

Install STN Express with Discover! window. One Setup Option is 

available for Network Server installs: 

· Softcopy documentation – copy the PDF User Guide to the 

server. 

Type the path to the server installation folder, or click the > button to 

browse. 

Click Install STN Express with Discover! to continue. 

The Setup program will then build the STN Express with Discover! folder. 

It will not create a Windows Start Menu item, nor will it create the 

EXPRESS.INI control file. These will be created during the Network Client 

setup (see below). 

The Setup program creates a special version of itself and stores it in the 

STN Express root folder (typically STNEXP) on the server. This program, 

SETUP.EXE, can be run by users to install STN Express with Discover! 

on their local machines. It will build the local STN Express folder structure 

and create a Windows Start Menu item for STN Express. It also builds the 

EXPRESS.INI control file and stores it in the local Windows folder. 

See the Changing SETUP.INF section below for important information 

about the network patch to the server isntallation. 

Sharing 

the server 

installation 

on the 

network 

Share the STN Express installation on the network. Client may refer to the 

network share by its UNC name or by mapping a drive letter to it. 

It is recommended that all files residing on the server be write protected 

from the network.


Changing 

SETUP.INF 

After the Network Server installation is complete, you may need to modify 

the contents of the setup control file for user installations. To do this, edit 

the file SETUP.INF located in the STN Express folder on the server. The 

following section should be verified. 

· [server] - verify that this section contains the proper network path 

to the server installation. This value is used as the default path for 

the Network User setup. If this value will not be consistent across 

all network user machines, e.g., on one client PC it is N:\STNEXP 

and another it is I:\STNEXP, leave this field blank (“Express=”). 

Installing STN 

Express on a 

client PC 

Each user of STN Express with Discover! should run SETUP.EXE from 

the server drive. Simply select the Network User option from the Setup 

Type section of the opening dialog box. 

The “Path to Network STN Express” is activated. Verify that it contains the 

appropriate path specification to the network folder for STN Express. 

Contact your network administrator if it does not specify the network folder 

for STN Express. 

Enter the appropriate storage location on the local PC in the following 

dialog box. The Setup program will then build the local STN Express with 

Discover! environment. 

The Setup program located on the CD may also be used; however, it 

contains a generic specification for network installations and further 

changes may be needed after it is complete. 

Upgrading to 6.0 

from a Network 

Server 

If you are currently running STN Express 5.0 from a network server on 

your client PC, first make sure the server installation has been updated to 

6.0. Then run setup.exe from the server. This gives you everything needed 

to use the new features.

G–4 Network Installation 

Information 

for Network 

Administrators 

If you wish to set up a standard set of logon procedures and preferences 

for all of your users, follow the steps below: 

1. Install STN Express with Discover! on the server as described 

above. Then perform a Network Client install on one user’s PC. 

2. Start STN Express with Discover! on the user’s PC and define 

options that you want all users to have, i.e., logon procedures and 

user preferences. 

3. Exit STN Express with Discover! and save changes when 

prompted. 

4. Copy the EXPRESS.INI file and any additional .INI files 

beginning with the letters “STN” from this PC’s WINDOWS folder 

to the server. Also, any files that are created in the USCRIPTS 

folder (as the result of Custom Logon or Logoff scripts) should 

also be copied to all client machines. They can then be copied to 

any user’s PC after a Network User setup has been done. 

Please note the following limitations: 

· Store any .INI files on the server, using a different name, e.g., 

name.NET. This will prevent any confusion when running the 

program. Users must copy these files to their WINDOWS folder 

and rename them to the original name. This is a requirement! 

· All users of STN Express must have STN Express with Discover! 

loaded in the same path on their local machines. For example, all 

users must have c:\stnexp as the root folder for STN Express with 

Discover!. The reason for this is that the EXPRESS.INI 

file contains path names for storing and accessing files. If this is 

not done, path specifications will be incorrect and STN Express 

with Discover! will not work properly. 

If you have any questions or problems, please contact your Help Desk.


Converting 

a Single-User 

Installation to 

a Network 

Share 

· Follow the steps in the Installing STN Express on a Server 

section of this Appendix to install the Network Server copy. 

· Follow the steps in the Installing STN Express on a Client PC 

section of this Appendix to convert each copy of STN Express 

with Discover! to a Network User copy. 

· Select the location where STN Express currently resides. The 

installation program upgrades the files and the program group to 

access STN Express with Discover! on the server. 

+ Only files provided by your previous STN Express installation 

programs are overwritten. Any structures, scripts, guided search 

strategies, or transcripts that you have created are unaffected by this 

installation. However, STN Express scripts that you have modified 

should be moved out of the STN Express directory. Changes to those 

files should be added to the new versions supplied with version 6.0.

Appendix 

H 

Overview 

Removing STN Express and Its Applications H–1 

Removing STN Express and 

Its Applications 

STN Express 6.0 includes an uninstaller program. See the ReadMe.txt file 

for details. If the uninstaller program is not available, STN Express may be 

removed manually. 

Removing 


From Your 

Hard Disk 

To remove STN Express from your hard disk, follow these steps: 

1. Copy or move all queries and transcripts that you want to keep to 

a safe location. 

2. Remove the STNEXP folder and all folders contained within. 

Consult the file Desetup.inf for a list of files installed by STN 

Express with Discover!. 

3. Remove Express.ini and all other Stnxxxxx.ini files from the 

WINDOWS folder. 

To remove the STN Express Start menu item: 

1. Right click on the Windows Task Bar. 

2. Click Properties. 

3. Select the Start Menu Programs tab. 

4. Click the Remove button. 

5. Scroll down the list to find the STN Express Group. Select this 

group. 

6. Click the Remove button.

H–2 Removing STN Express and Its Applications 


Applications 

STN Express with Discover! consists of the following distinct programs: 

Program icon Program name Function 

Express.exe 

Stnpsi.exe 

Stnsetup.exe 

Stnterm.exe 

Stnacct.exe 

Stnedit.exe 

Stnwpi.exe 

Stnocc.exe 

The main program and toolbar 

provide access to STN 

Express programs. Logon 

setups and General 

Preferences are stored in the 

file: express.ini. 

Structure Drawing. 

Preferences are stored in 

stnpsi.ini. 

Logon setup program. Use it 

to create and change logon 

setups. Its configuration file is 

stnsetup.ini, but the logon 

setups themselves are stored 

in express.ini. 

STN Online and Results. 


stnterm.ini. 

STN Accounting. 


stnacct.ini. 

STN Edit (text editor). Its 

configuration file is stnedit.ini. 

Fragmentation Code 

Generator for Derwent WPI 

queries. 

Other Code Concepts 

program for Derwent WPI 

queries. 

Applications may be removed from the STN Express directory if you do 

not intend to use them.

Removing STN Express and Its Applications H–3 


Folders and 

Files 

Additional folders and files that are added to your hard disk include: 

Folder or File 

Content 

.dll files 

.dta files 

.hlp files 

Networks file 

Pssfiles 

Queries 

Scripts 

Template 

Trnscript 

Umanual 

Uscripts 

Library files essential to the function of the 

applications 

Data files used in Derwent WPI Fragmentation 

Code Strategy generation 

STN Express Help files for the Windows help 

system. 

Data file for supported communication networks 

Scripts that implement specific (Predefined 

Search Strategies) 

Default location for storing your structure 

queries 

STN Express scripts for connecting through 

supported networks and logging on to 

supported online hosts 

Pre-drawn chemical structure templates used 

for building structure queries. Standard (.std), 

stereo (.str), and SpecInfo (.spe) templates are 

included. 

Default location for storing your STN Express 

session transcripts, reports, and tables 

Electronic User Guide in PDF format 

Scripts and command files written by you; the 

STN accounting file; and other user-specific 

files

Appendix 

I 

Overview 

Troubleshooting 

Troubleshooting I–1 

This section provides answers to common problems that you may 

encounter while using STN Express with Discover!. You may also visit 

CAS Software Support on the Web at http://www.cas.org/Support/ 

software.html. 

Problems 

with 

Transcripts 

This information pertains to traditional, .trn transcripts, not to transcripts that 

are captured as RTF. 

STN Express transcripts that contain structure diagrams are stored in two 

main files. You provide the name for the files when the transcript is created. 

One file, with a .trn extension, contains the text of the transcript. The other 

file, with a .gra extension, contains the graphic (structure diagrams) part of 

the transcript. For example, if you name the transcript STN search.trn, then 

that file contains the text part of the transcript, and the file STN search.gra 

contains the structure diagrams for the transcript. If you downloaded 

images, there will be one .tif, .jpg, or gif file for each image. 

1. Graphics (structure diagrams and downloaded images) are missing 

from a transcript on your screen 

· STN Express Browse Transcript knows how to combine the 

text and graphics files into one display. If graphics are missing, 

check to see that both the .trn and .gra files exist and are 

stored in the same folder. 

· STN Express Edit Transcript reads only the text portion (.trn 

file) of a transcript and cannot display graphics. 

· If you open a transcript in Microsoft Word or another program, 

be sure to Export the transcript first. The export process 

combines the .trn, .gra, and .tif files into one RTF file. 

2. Graphics (structure diagrams and TIFF images) are missing from a 

printed transcript 

· If graphics are missing from a printed transcript, check for the 

existence of the files as noted above. 

· Print the transcript from Browse Transcript or from the main 

menu bar (Results -> Print Transcript). 

· Because STNEdit does not display graphics, it cannot print 

them. 

· Go to Terminal Emulation Preferences, the Online tab, and 

check the Print Chemical Structures box.

I–2 Troubleshooting 

3. Line wrap in printed transcripts 

If you see the ends of lines wrapping to the start of the next line, 

check the margins and font size. By default, STN Express uses a 10 

pt. Courier New font and 0.75-inch left and right margins. To solve 

the line-wrap problem, switch to a smaller font or use smaller left and 

right margins. To change the font, select Preferences, then STN 

Online and Results, and then the Colors/Fonts/Scaling tab. To 

change the margins while browsing a transcript, select Page Layout 

from the File menu. 

Downloaded 

Images 

TIFF, JPEG, and GIF images, such as patent drawings or complete page 

images, are available in several STN files. See the appropriate section in 

Chapter 4 for more information. 

1. Problems downloading images 

For faster TIFF, JPEG, and GIF image downloads in STN files such 

as CAOLD, DEMAS, and WPINDEX, use the default setting of 

Long Packets and a packet size of 4000 that is found on the 

Online tab of the STN Online and Results Preferences. If you 

see Kermit error messages, try reducing the packet size. 

A packet size of 4000 is not recommended for low-speed 

connections. Recommendations are: 

Connection 

Speed 

Packet 

Size 

Internet/Winsock 4000 

9600 and higher 4000 

2400 and up 1000 

1200 and up 500 

2. Locating downloaded images 

When you download images while you capture a transcript, the 

images are named the same as your transcript plus a three-digit 

number. The image files have appropriate extensions (.tif, .jpg, .gif) 

in their names. 

When you download images when no transcript is captured, the 

image files are named starting with Image001 and continuing with 

Image002, etc. Appropriate extensions (.tif, .jpg, .gif) are used.


3. TIFF images print smaller than expected 

· When TIFF images are printed in the context of a transcript, 

they appear smaller than you might desire. Check the 1 TIFF 

Image/page box on the Page Layout dialog box that opens 

during the transcript printing process. 

· When TIFF images are printed from the TIFF image viewer, 

they are printed at a size that is proportional to the viewer’s 

“zoom factor”. For the largest possible printed image, zoom in 

(View -> Zoom In) as far as possible and then select File -> 

Print. 

Modem 

Problems 

Communications problems include characters lost from answer displays, 

corrupt structure diagrams, and difficulty downloading images. These 

problems occur much more frequently under modem connections than 

with Internet/Winsock connections. 

Missing characters and corrupt structure diagrams: 

· For modem speeds of 4800 baud and higher, use hardware 

(RTS/CTS flow) control. For modem speeds under 4800 baud, 

use software (XON/XOFF) flow control. The flow control setting 

is found in your modem Control Panel or in your STN Express 

logon setup. 

· For modem speeds of 9600 baud and higher, the correct 

communications parameters are data bits: 8; parity: none; stop 

bits: 1. 

· Make sure you have a current version of the driver for your 

modem brand and model. 

Not Able to 

Connect - 

General 

Script SYSCNCT - Unable to open command file pop-up message 

Terminal Emulation is not able to locate a script that is needed to log on to 

the host. The most likely cause is that the path to the Predefined Scripts 

folder is incorrect in General Preferences. To check the path, go to the 

main STN Express menu bar, select Setup -> Preferences -> General. 

The Predefined Scripts box must contain the location of a folder that holds 

the scripts that are packaged with STN Express. By default, the path is 

C:\Program Files\Stnexp\Scripts, but your installation location might be 

different. The paths in General Preferences can be rendered incorrect 

by moving the STN Express installation folder from one place to another.


Not able to 

connect - 

modem 

In general, look for messages in the Terminal Emulation window that point 

to the problem. Check to see that the modem has power and is connected 

to the computer and a working telephone line. 

1. The modem is not responding to modem commands message 

· Check to make sure an external modem is turned on. 

· Check to make sure the modem is connected to a serial port on 

the computer. 

· Check that COM port setting in the STN Express logon setup is 

the one to which the modem is attached. 

2. The telephone line is not providing a tone for dialing message 

· Check that the modem is connected to a live, working phone 

line. 

· Check that the phone line is not being used by a telephone or 

another modem (is the line busy?). 

· If you selected a modem from the Connect via list in your logon 

setup, try selecting the modem’s COM port instead. 

Not able to 

connect – 

Internet 

In general, look for pop-up messages and messages in the Terminal 

Emulation window that point to the problem. 

1. Unable to Establish Connection pop-up message 

· Check the Host Name or IP address in the logon setup. Be 

sure there are no typing mistakes or leading or trailing spaces. 

If you’re not able to connect to the specified host name, try the 

equivalent IP address. 

· Try to connect to the Host Name or IP address using the 

Windows telnet.exe program. This tests the ability to connect 

without STN Express. 

· Your connection attempt might be hitting a firewall or gateway. 

Contact your network administrator for instructions on how to 

use telnet outside your organization’s network. 

2. Terminal Emulation hangs, or the connection times out 

· See #1 immediately above. 

3. Dial-Up Networking does not launch 

· The DUN connection might already be established. 

· Try establishing the dial-up connection first, outside of STN 

Express. If the connection cannot be made, the problem is 

probably in the DUN configuration or modem Control Panel.


Unexpected 

behavior after 

reconnecting 

Always begin and complete your STN session using the same 

telecommunications software. If you initially logged on through STN 

Express, end your session through STN Express. For example, if you 

initially connect to STN using Windows telnet, then disconnect, and then 

reconnect to the same session using STN Express, you will observe 

abnormal behavior in STN Express. 

Problems 

switching from 

Generic DARC 

to Questel 

If you have trouble switching from the Generic DARC system to Questel 

using the BI command, log off from Generic DARC and then connect to 

Questel directly and log on. 

Creating a 

Setup 

1. Error opening Network Control file pop-up message after clicking 

New or Modify 

The file Express.ini is stored in the Windows (Windows 95/98/Me) 

folder or the WinNT folder (Windows NT 4.0/2000). In Express.ini, 

in the [Paths] section, the value of the express= parameter must be 

the STN Express installation folder. By default this folder is 

C:\Program Files\Stnexp. The parameter can be incorrect if the 

STN Express installation folder is moved from one place to another. 

To correct the problem, edit Express.ini and change the value of the 

express= line to the location of your STN Express installation. 

2. The OK button is grey 

Some piece of required information is missing. A Setup Name is 

required for every logon setup. A Logon Method other than None 

and a Primary Phone # are required for each setup that uses a 

modem.


Structure 

Upload 

1. General problems 

· Try uploading the structure again. Line noise or a poor 

connection can cause the upload to fail. 

· Communications settings might be incorrect. If you are 

experiencing data loss in general, see the Communications 

problems - modem section above. 

· Be sure that STN recognizes your terminal as STN Express. 

Always use the STNLOGON script to complete your log on to 

STN. 

· The problem could be due to the particular structure. If you can 

successfully upload other structure queries, report the problem 

structure to the Help Desk. 

2. Fatal Kermit Error pop-up message 

· See the information in #1 immediately above. 

· The maximum size of a structure query for uploading might have 

been exceeded. Modify your query to make it smaller, or use the 

STRUCTURE command on STN. 

Additional 

Help 

If you need further assistance, contact the Help Desk for your STN 

Service Center: 

· Go to the STN Express Help menu, select Request Help, and 

then select your STN Service Center to send email. 

· Telephone your Help Desk as listed in Chapter 1, Introduction. 

Please have the following information available when you call or write. 

· STN Express with Discover! version number, e.g., 6.0a. To find 

the exact version, go to the Help menu on the main menu bar and 

select About STN Express. 

· Operating System, e.g., Windows NT 4.0 

· System information, including amount of memory (RAM) 

· Specific information about your problem.

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