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Administrator as part of the data about a reaction. Maps are used during searching to resolve certain types of structure search hits. Consider a simple esterification reaction: O OH OH Does the ester oxygen come from the acid or the alcohol? You specify the fate of individual atoms through an atom-to-atom map. In reality, the ester oxygen in this reaction originates in the alcohol, so the atom-to-atom map looks like this: O O H 2 O NOTE: For information about specifying atom-to-atom maps with ChemDraw, see the ChemDraw User’s Guide. Searching for Reactants If you know what starting materials you are interested in but don’t know their products, you might perform a reactants query. A reactants query is very similar to a reaction search, except that there is nothing to the right of the arrow. For example, consider the query: O 1 3 O Rxn 2 OH 4 5 OH 6 1 By matching numbers across the arrow, you can see where atoms move during the course of the reaction. The other reaction (not observed experimentally), where the ester oxygen comes from the acid, would be mapped like this: 1 3 O 2 OH 4 5 Rxn OH 6 2 Rxn O 6 ChemFinder uses atom-to-atom map information to determine reacting centers for reactions. If only some atoms are mapped, ChemFinder uses that information and does not worry about the specific fates of the other atoms. For example, if you don’t know (or don’t care) about the mapping of some atoms, you can leave them unspecified in the atomto-atom map. By default, atom-to-atom mapping is not displayed within ChemFinder. To turn on this display, select Atom-to-Atom Map on the Structure sub-menu of the View menu. For more information, see “Setting Preferences” on page 341. 1 3 O 3 O 2 O Rxn 4 5 5 H 2 O 4 H 2 O 6 O O If you are doing a substructure search, this finds any reactions in which maleic anhydride or a compound containing a maleic anhydride substructure is consumed or transformed. Searching for Products If you know the desired end product but not how to get there, you can do a products query. A products query is similar to a reaction search, except that there is nothing to the left of the arrow. For example, consider the query: If you are doing a substructure search, this finds any reactions in which bicyclo[2.2.1]heptane or a compound containing this substructure is produced. 324•Searching CambridgeSoft Reaction Searches
Searching for Intermediates Rarely, you may be looking for reactions for which you only know something about an intermediate. An Intermediate Search is very similar to a normal reaction search, except that there are arrows on both sides of the target structure. For example, consider the query: R C C O This finds any reactions containing the Ketene structure shown as an intermediate. NOTE: ChemFinder cannot predict products or intermediates of reactions. It finds this information only if it is already present in the database. Combined Searches You can combine structure searching with text searching to find a specific class of compounds. For example, you may want to find all compounds in the database whose names end in mycin and whose structures contain a phenyl ring. Because you are entering multiple queries in different data boxes, there is an implicit AND condition between data items in different fields. To perform a combined search: 1. From the Search menu, choose Enter Query to clear the form. 2. Enter the structural query, if any. 3. Enter the text and/or numeric queries in the appropriate boxes. 4. From the Search menu, choose Find. An example of combined searching: Suppose you want to find all molecules in the CS_Demo database that contain a benzene ring and which have names related to penicillin. 1. From the Search menu, choose Enter Query to clear the form. 2. Draw a benzene ring. 3. Enter *penicillin* in the Molname field. 4. With the Substructure option selected, choose Find from the Search menu. You get 2 hits of molecules whose names contain penicillin and whose structures have an aromatic ring of six carbon atoms. NOTE: In a combined search, progress reports are given only during the structure search part. When the counters at the bottom of the screen are advancing, structures are being searched. You can press Esc to end a search during the structure searching. You cannot end a search during the SQL searching by pressing Esc. SQL Searches SQL (Structured Query Language) can be used to create powerful searches. The details of the language are not discussed here. Queries beginning with a backslash (\) are taken as straight SQL, and passed directly to the database as the WHERE clause of the SQL query. These must contain column names and punctuation as dictated by SQL. For example, a valid query might be \[molname] like 'benz*' and [bpoint] > 200. A straight SQL query may be entered in any box of the form which contains non-structural data. The SQL query is not associated with the box in which it is entered. Searching Procedures ChemFinder Searching includes the following steps: ChemOffice 2005/ChemFinder Searching • 325 Combined Searches
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ChemOffice.Com ® ChemOffice ® Che
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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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Administrator the activation each t
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Administrator The following table d
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Administrator • Stereo Pairs—A
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Administrator • Bond Angles—Dis
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator • In the Model Sett
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Administrator modes and color setti
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Administrator 26 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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3. Move the pointer over the C-C bo
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Administrator 5. Press the Enter ke
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Administrator In the Measurements t
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Administrator Tutorial 7: Docking M
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Administrator To save the iteration
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The allyl radical, CH 2 =CHCH 2·,
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Administrator Determine the raw spi
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Administrator atoms are relatively
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator To use the same text
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Administrator Example 2. Building a
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Administrator copied into blank tab
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Administrator 3. Type the atom type
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Administrator Clean Up Structure or
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Setting Serial Numbers this step, y
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Administrator Refining a Model Afte
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Administrator Selecting Multiple At
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Administrator New in Chem3D version
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Administrator Dragging moves atoms
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Administrator 3. Hold down the Shif
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To position a plane in your model p
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Administrator • Second Positioned
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Administrator For example, consider
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Administrator • From the Computat
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Administrator Example: To examine t
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Administrator • Molecular mechani
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Administrator 6. The modified value
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Administrator A variety of other ba
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Administrator Molecular wave functi
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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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If you want to … Then Click … A
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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 The following table c
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Administrator TRIPLET QUARTET QUINT
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Administrator Chemical symbol ++ ba
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Administrator 4. Click Run. A new m
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Administrator Minimizing Energy Min
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Administrator criteria, to optimize
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Administrator 6. Hold down the S ke
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Administrator Dipole Moment The dip
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Administrator Molecular Surfaces Mo
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Administrator 3. Click in the model
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Keyword Description 7. On the Prope
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Administrator Hyperfine Coupling Co
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Administrator 194•MOPAC Computati
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Administrator If you want to … re
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Administrator In the Results In tex
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Administrator Repeating a Gaussian
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Administrator To specify the calcul
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Administrator 3. Click Open. The ap
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Property Description Property Descr
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Administrator To perform property c
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Administrator • From the ChemOffi
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Administrator 220•Introduction Ca
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Administrator Screen Element Table
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Administrator • From the View men
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Administrator A form displays data
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. In this tutorial, you learn to cr
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Administrator The database opens, a
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9. Click the Form tab. There should
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to see some of the information avai
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Administrator The Table view appear
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+ The ISICCR database opens in Chem
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Administrator To search over a list
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When you release the mouse button,
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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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The framed data box is labeled. NOT
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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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To line up objects on a form: Admin
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Administrator to those usernames. M
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Page 322 and 323: Creating Fields Administrator 4. Fr
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Page 334 and 335: Administrator The plot appears in a
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Page 340 and 341: Administrator 308•Visualizing Dat
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Administrator For more information
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Administrator The Open Chemical Str
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Administrator 3. From the Molecules
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Administrator To use the Search Opt
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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 Working with the User
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Administrator Showing and Hiding Co
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Administrator • Right-click any b
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Administrator If your system config
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Administrator Your system configura
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Administrator Working with Template
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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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Administrator Clicking the Changes
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Administrator In some configuration
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Administrator 452• Changes and Au
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Administrator Advanced Text Searchi
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Administrator 4. A new Section List
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Administrator Managing the Audit Se
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Administrator The field appears in
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Administrator For example, if there
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Administrator 506• Managing Secti
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Administrator Example 1 In this exa
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Administrator See the following top
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Administrator Associating a list of
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Administrator • Username - An opt
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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 reactants and product
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Administrator contained collection
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Administrator Chemical Structure Se
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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 Desired Result Remove
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Administrator 596• Managing E-Not
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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 14 13 H 2.197 -0.8229
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Administrator COMPND ATOM HETATM CO
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Parameter Table Use Parameter Table
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O O Bond Type Description Administr
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Administrator 686• Structural Que
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Administrator 706• CS Oracle Cart
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Administrator Atom-to-Atom mapping
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Administrator Combi experiments 367
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Administrator Creating (continued)
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Administrator Dihedral type field 6
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Administrator Exporting (continued)
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Administrator Frame interval contro
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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 Search Details prefer
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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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