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Administrator Refining a Model After building a 3D structure, you may need to clean it up. For example, if your model was built without automatic rectification, atom type assignment, or standard measurements, you can apply these as a refinement. Rectifying Atoms To rectify the selected atoms in your model: • From the Structure menu, choose Rectify. Hydrogen atoms are added and deleted so that each selected atom is bonded to the correct number of atoms as specified by the geometry for its atom type. This command also assigns atom types before rectification. The atom types of the selected atoms are changed so that they are consistent with the bound-to orders and bound-to types of adjacent atoms. Cleaning Up a Model Normally, Chem3D creates approximately correct structures. However, it is possible to create unrealistic structures, especially when you build strained ring systems. To correct unrealistic bond lengths and bond angles use the Clean Up Structure command. To clean up the selected atoms in a model: • From the Structure menu, choose Clean Up . The selected atoms are repositioned to reduce errors in bond lengths and bond angles. Planar atoms are flattened and dihedral angles around double bonds are rotated to 0 or 180 degrees. 68 •Building and Editing Models <strong>CambridgeSoft</strong> Refining a Model
Chapter 4: Manipulating Models Overview Chem3D provides tools to manipulate the models you create. You can show or hide atoms and select groups to make them easier to manipulate. Molecules can be rotated, aligned, and resized. Selecting Most operations require that the atoms and bonds that are operated on be selected. Selected atoms and bonds are highlighted in the model display. You can change the default highlight color in the Model Settings dialog box. Model Explorer tab Colors and Fonts tab Set Highlight Color To select an atom using the Model Explorer: 1. Open the Model Explorer. 2. Select the atom in the Explorer. The atom is selected in the model. Any previously selected atoms or bonds are deselected. Selecting Single Atoms and Bonds You can select atoms and bonds in the model window or by using the Model Explorer. If the Model Explorer is not active, open it from the View menu. To select an atom or bond in the display window: 1. Click the Select tool . 2. Click the atom or bond. Any previously selected atoms and bonds are deselected. When you click a bond, both atoms on the bond are selected. <strong>ChemOffice</strong> 2005/Chem3D Manipulating Models • 69 Selecting
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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 • Bond Angles—Dis
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Administrator The Building Toolbar
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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 staggered form. The m
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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 improvements in each
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Administrator TRIPLET QUARTET QUINT
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Administrator criteria, to optimize
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Administrator Molecular Surfaces Mo
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to see some of the information avai
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A data source tree appears, contain
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Administrator When the selection to
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Administrator to those usernames. M
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Administrator Creating Tables There
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Administrator ChemFinder creates a
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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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The general procedure for importing
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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 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 • Equivalents - the
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Administrator Ethanol was selected,
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Administrator Type in the AutoText
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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 Replacing a Spectrum
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Administrator you enter an invalid
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Administrator 452• Changes and Au
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Administrator 2. Select Remove Prop
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Administrator Advanced Text Searchi
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Administrator Searching For ... Ret
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3. Click the Search In... checkbox
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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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A menu appears. 2. Select Box Prope
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Showing the Name of a Box To show t
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Administrator contained box accordi
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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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Managing Search Fields Administrato
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Administrator To access the Add-In
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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 2. If Inherits Securi
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To change the Transition Security P
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Administrator To disable inherited
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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 • Add Reactant tabl
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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 14 13 H 2.197 -0.8229
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Parameter Table Use Parameter Table
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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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