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Administrator The following table describes the Model Build controls Control Correct Atom Types Rectify Description Determines whether atom types are assigned to each atom as you build. Atom types, such as “C Alkane” specify the valence, bond lengths, bond angles, and geometry for the atom. Determines whether the open valences for an atom are filled, usually with hydrogen atoms. NOTE: For more information about atom types, standard measurements, and rectification, see “Model Building Basics” on page 20. Building with the ChemDraw Panel Chem3D 9 makes it easier than ever to create or edit models in ChemDraw. The ChemDraw panel is activated from the View menu. Using ActiveX technology, it puts the functionality of ChemDraw Pro at your fingertips. To add a new structure to Chem3D: Apply Standard Measurements Fit Model to Window Detect Conjugated System Bond Proximate Addition (%) Determines whether the standard measurements associated with an atom type are applied as you build. Determines whether the entire model is resized and centered in the model window after a change to the model is made. When selected, all bonds in a conjugated system are set at a bond order of 1.5. When unselected, bonds are displayed as drawn. Does not affect previously drawn structures. Determines whether a bond is created between a selection of atoms. For more information see “Creating Bonds by Bond Proximate Addition” on page 62. 1. Open the ChemDraw Panel by selecting it from the View menu. The ChemDraw panel appears on the right of the model window. 2. Click in the panel to activate it. The Tools palette appears. TIP: If you don’t see the Tools palette, right-click in the ChemDraw panel, and check the View menu to see that it has been activated. There should be a check mark next to Show Main Tools. While you are at it, you might want to activate other toolbars. Activating the General tools toolbar, for example, will give you access to undo/redo commands. 3. Build the structure. The model appears simultaneously in both the ChemDraw and Chem3D model windows. Unsynchronized Mode By default, the ChemDraw panel works in synchronized mode. In this mode, your model appears simultaneously in the ChemDraw panel 52 •Building and Editing Models <strong>CambridgeSoft</strong> Building with the ChemDraw Panel
and in Chem3D. Editing either model changes the other automatically. This affords maximum editing flexibility. To turn off synchronized mode: • Click the Synch button at the top left of the ChemDraw panel. The button toggles synchronization on and off. To copy a model to Chem3D, click either the Add or Replace icon. Name=Struct The ChemDraw panel has a Name=Struct window that allows you to build models by entering a chemical name or SMILES string. You can also copy names or SMILES strings from other documents and paste them, either into the Name=Struct window, or directly into the Chem3D model window. TIP: You can also paste chemical formulas into the Chem3D model window. Be aware, however, that a formula may not represent a unique structure, and the results may not be correct. Building with Other 2D Programs You can use other 2D drawing packages, such as ISIS/Draw to create chemical structures and then copy them into Chem3D for automatic conversion to a 3D model. To build a model with 2D drawings: 1. In the source program, copy the structure to the clipboard. 2. In Chem3D, from the Edit menu, choose Paste. The 2D structure is converted to a 3D model. The standard measurements are applied to the structure. For more information see “Appendix E: 2D to 3D Conversion.” NOTE: You cannot paste from ISIS/Draw into the ChemDraw panel, only into the Chem3D model window. You can, however use the synchronize control to add the model to the ChemDraw panel. You can also cut-and-paste, or drag-and-drop, models to and from ChemDraw to Chem3D or the ChemDraw panel. See “Transferring to Other Applications” on page 123 for more information on pasting into other applications. Non-bond or atom objects copied to the clipboard (arrows, orbitals, curves) are ignored by Chem3D. Superatoms in ISIS/Draw are expanded if Chem3D finds a corresponding substructure. If a corresponding structure is not found, you must define a substructure. For more information see “Defining Substructures” on page 614. Building With the Bond Tools Use the bond tools to create the backbone structure of simple models. Bond tools always create bonds that terminate with carbon atoms. Hydrogens display automatically by default. You can hide them to reduce clutter. You can change the carbons or hydrogens to other elements after you create the generic model. To create a model using a Bond tool: 1. Choose a bond tool. The Single Bond tool is used in this example. 2. Point in the model window, and drag in the direction you want the bond to be oriented. 3. Release the mouse button to complete the bond. <strong>ChemOffice</strong> 2005/Chem3D Building and Editing Models • 53 Building With the Bond Tools
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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 To export to MS Word:
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Administrator If the user wants to
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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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