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Administrator Example 2. Building a Model with a Substructure and Several Other Elements To build a model with substructures and other elements: 1. Type PrNH2 into a text box with no atoms selected. 2. Press the Enter key. A model of propylamine appears. The appropriate bonding site for the Pr substructure is used for bonding to the additional elements NH2. The alpha form of the neutral polypeptide chain composed of Alanine, Glycine, and Phenylalanine appears. NOTE: You can use the amino acid names preceded with a ß– to obtain the beta conformation, for example Hß–Alaß–Glyß–PheOH. To generate the ß character, type Alt+0223 using the number pad. The appropriate bonding and dihedral angles for each amino acid are pre-configured in the substructure. Example 3. Polypeptides Use substructures for building polymers, such as proteins: 1. Type HAlaGlyPheOH into a text box with no atoms selected. The additional H and OH cap the ends of the polypeptide. If you don’t cap the ends and automatic rectification is on, Chem3D tries to fill the open valences, possibly by closing a ring. 2. Press the Enter key. Ring closing bonds appear whenever the text in a text box contains two or more open valences. TIP: To better view the alpha helix formation, use the Trackball Tool to reorient the model to an end-on view. For more information see “Trackball Tool” on page 75. To change the polypeptide to a zwitterion: 1. Select the Text tool. 2. Click the terminal nitrogen. A text box appears over the nitrogen atom. 3. Type + and press the Enter key. The charge is applied to the nitrogen atom. Its atom type changes and a hydrogen atom is added. 4. Click the terminal oxygen. A text box appears over the oxygen atom. 5. Type - in the text box and press the Enter key. 58 •Building and Editing Models <strong>CambridgeSoft</strong> Building With The Text Tool
The charge is applied to the oxygen atom. Its atom type changes and a hydrogen atom is removed. For amino acids that repeat, put parentheses around the repeating unit plus a number rather than type the amino acid repeatedly. For example, type HAla(Pro)10GlyOH. 4. Press the Enter key. The substructure replaces the selected atom. For example, to change benzene to biphenyl: 1. Click the atom to replace. A text box appears. Example 4. Other Polymers The formation of a PET (polyethylene terephthalate) polymer with 4 units (a.k.a.: Dacron, Terylene, Mylar) ia shown below: • Type OH(PET)4H into a text box with no atoms selected and press the Enter key. The H and OH are added to cap the ends of the polymer. 2. Type Ph. 3. Press the Enter key. Replacing an Atom with a Substructure The substructure you use must have the same number of attachment points as the atom you are replacing. For example, if you try to replace a carbon in the middle of a chain with an Ethyl substructure, an error occurs because the ethyl group has only one open valence and the selected carbon has two. To replace an individual atom with a substructure: 1. Click the Text tool. 2. Click the atom to replace. A text box appears. 3. Type the name of the substructure to add (case-sensitive). Building From Tables Cartesian Coordinate tables and Z-Matrix tables can be saved as text files or in Excel worksheets. (See “Z-matrix” on page 24 and “Cartesian Coordinates” on page 24 for more information.) Likewise, tables from text files or worksheets can be <strong>ChemOffice</strong> 2005/Chem3D Building and Editing Models • 59 Building From Tables
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Chapter 31: Changes and Audit Trail
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Administrator Tutorial 7: Docking M
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Administrator Connection Table . .
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Administrator Specifying Properties
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Administrator Undoing Changes . . .
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Administrator Chapter 28: Introduci
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Administrator Atom Properties . . .
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Administrator Deleting a Field Type
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Administrator Example 2. . . . . .
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Administrator Reaction Center . . .
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Administrator In addition to browsi
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Administrator Microsoft®Windows®
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Administrator Truncated-Newton-Raph
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Molecular Design Limited MolFile (.
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Administrator 124•Printing and Ex
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Administrator • Semiempirical Ext
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Method Type Advantages Disadvantage
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Administrator • Molecular mechani
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Administrator The van der Waals int
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Administrator 6. The modified value
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Administrator A variety of other ba
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Administrator activation barriers.
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3. From the Calculations menu, poin
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Administrator Intermediate status m
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Administrator staggered form. The m
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Administrator During dragging, the
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Compute Properties The Compute Prop
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Administrator C(2)-C(3)-C(4) bond a
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Administrator The procedures assume
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Administrator improvements in each
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Administrator • Overall errors in
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Administrator Minimizing Energy Min
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Administrator Molecular Surfaces Mo
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Property Description Error Message
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Administrator Screen Element Table
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to see some of the information avai
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Administrator To search over a list
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Administrator 250•ChemFinder Tuto
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The Open dialog box appears. To cho
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A data source tree appears, contain
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ChemFinder saves the form with a .c
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Administrator To save a metafile fr
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Administrator • Rich Text—displ
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Administrator Adding a Data Box Men
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Administrator Customizing Numbers U
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Administrator When the selection to
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Administrator to those usernames. M
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Administrator • In the new dialog
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Administrator 282•Relational Data
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Administrator Creating Tables There
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Administrator atoms contained in th
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Administrator • If you are editin
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Administrator The record is permane
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Administrator Context menu options
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Administrator Using ChemDraw's Atom
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Administrator For more information
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Administrator 3. From the Molecules
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Administrator • Enhanced table of
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Administrator In addition, this gui
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Administrator 388• Introducing E-
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Administrator You can organize coll
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Administrator Your system configura
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Administrator Desired Result Change
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Administrator To export to MS Word:
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Administrator 410• E-Notebook Use
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Administrator NO 2 NO 2 Me Me HC(OE
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Administrator • Top of Arrow as R
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Administrator • Equivalents - the
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The example below shows the Prepara
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Administrator Ethanol was selected,
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Administrator Type in the AutoText
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Adding Properties to Property Lists
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Type of Measurement Permitted Units
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3. Enter the URL and click OK. Work
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Administrator A new Ancillary Data
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Administrator Replacing a Spectrum
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Administrator you enter an invalid
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Administrator Type of Measurement m
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Administrator 4. The spreadsheet ap
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5. Click the section menu icon. The
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Administrator Clicking the Changes
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Administrator 452• Changes and Au
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Administrator Advanced Text Searchi
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Administrator Searching For ... Ret
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Administrator The Collection Tree a
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2. Select Session Manager.... The S
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Administrator A new section type ap
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Administrator The field appears in
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Administrator Example 1 In this exa
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Administrator Associating a list of
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Administrator • Username - An opt
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Administrator from the Property dro
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Administrator The Field Properties
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Administrator 3. Right-click the Ta
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Administrator • SupplierID - the
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Administrator To access the Add-In
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Administrator In the query table fi
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Administrator 546• Managing Field
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Administrator contained collection
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Administrator Chemical Structure Se
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Administrator To add states to a co
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• Removing a Transition Listener
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Administrator • Unlocked Contents
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Administrator If the user wants to
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Administrator To view the export te
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Administrator To edit this data, 1.
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Administrator Setting the Region fo
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Administrator 584• User Administr
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Administrator 2. If Inherits Securi
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Administrator Desired Result Remove
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Administrator 596• Managing E-Not
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Administrator Section Listeners E-N
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Administrator 604 • CambridgeSoft
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Administrator Accessing the Online
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Administrator The CS ChemOffice SDK
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Administrator Troubleshooting This
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Administrator Defining Substructure
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Administrator If an atom can be ass
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Administrator Example 3 In Example
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Administrator 14 13 H 2.197 -0.8229
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Administrator Connection tables by
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Administrator Line 4e: C 1.53597 1
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Parameter Table Use Parameter Table
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O O Bond Type Description Administr
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Administrator 706• CS Oracle Cart
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Administrator Combi experiments 367
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Administrator Dihedral type field 6
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Administrator Exporting (continued)
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Administrator Mol_ID field 287 Mola
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Administrator Opening (continued) p
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Administrator Property query and ta
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Administrator Redo command 269, 299
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Administrator Sextic bending consta
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Administrator Subforms (continued)
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Administrator User interface 9 User
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Administrator xxxviii• CambridgeS
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CAMBRIDGESOFT ChemOffice Desktop to
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CS ChemOffice Software Suites ChemO
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DESKTOP CS E-Notebook Electronic Jo
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DESKTOP CS ChemDraw Chemical Struct
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DESKTOP CS Chem3D Molecular Modelin
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DESKTOP CS ChemFinder Searching and
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DESKTOP CS ChemInfo Reference and C
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ENTERPRISE ChemOffice WebServer Ent
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ENTERPRISE Oracle Cartridge Enterpr
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KNOWLEDGE E-Notebook Enterprise Des
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KNOWLEDGE Document Manager Desktop
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KNOWLEDGE 21CFR11 Compliance Electr
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RESEARCH & Registration System Chem
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RESEARCH & Inventory Manager Chemic
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RESEARCH & CombiChem Enterprise Des
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RESEARCH & BioAssay HTS Biological
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RESEARCH & BioSAR Browser Biologica
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CHEMICAL ChemACX Database Available
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CHEMICAL The Merck Index Chemistry
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CHEMICAL Chemical Databases Referen
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CONSULTING & Consulting & Services
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CS Software Problem Report For fast
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