Chem3D Users Manual - CambridgeSoft

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Administrator 3. Type the atom type to which you want to change the selected atoms. 4. Press the Enter key. The bond orders of the bonds change to reflect the new atom types. To change several bonds at once: 1. Open the ChemDraw panel and click in it to activate the ChemDraw control. 2. Choose either selection tool, Lasso or Marquee. 3. Click the first bond to be changed, then use Shift+Click to select the others. 4. Right-click in the selected area, and choose the bond type. Pairs of atoms whose distance from each other is less than the standard bond length, plus a certain percentage, are considered proximate. The lower the percentage value, the closer the atoms have to be to the standard bond length to be considered proximate. Standard bond lengths are stored in the Bond Stretching Parameters table. To set the percentage value: 1. From the File menu, choose Model Settings. The Chem 3D Model Settings dialog box appears. 2. Select the Model Build tab. 3. Use the Bond Proximate Addition% arrows to adjust the percentage added to the standard bond length when Chem3D assesses the proximity of atom pairs. You can adjust the value from 0 to 100%. If the value is zero, then two atoms are considered proximate only if the distance between them is no greater than the standard bond length of a bond connecting them. For example, if the value is 50, then two atoms are considered proximate if the distance between them is no greater than 50% more than the standard length of a bond connecting them. 5. Click in the Chem3D window to complete the action. Creating Bonds by Bond Proximate Addition Atoms that are within a certain distance (the bond proximate distance) from one another can be automatically bonded. Chem3D determines whether two atoms are proximate based on their Cartesian coordinates and the standard bond length measurement. To create bonds between proximate atoms: 1. Select the atoms that you want tested for bond proximity. 2. From the Right-click menu, point to Bond(s) and choose Proximate. If they are proximate, a bond is created. Adding Fragments A model can be composed of several fragments. If you are using bond tools, begin building in a corner of the window. 84 •Building and Editing Models CambridgeSoft Adding Fragments
If you are using the Text tool: 1. Click in an empty area of the window. A text box appears. 2. Type in the name of an element, atom type, or substructure. 3. Press the Enter key. The fragment appears. For example, to add water molecules to a window containing a model of formaldehyde: 1. Click the Text tool. 2. Click in the approximate location you want a water molecule to appear. A text box appears. 3. Type H2O. 4. Press the Enter key. The fragment appears. 5. Double-click in a different location to add another H 2 O molecule. View Focus As models become large, keeping track of the section you are working on becomes more difficult. With version 9.0.1, Chem3D adds the notion of “view focus”, defined as the set of atoms that the user is interested in working on. By default, the view focus includes all of the atoms in the model. To change the view focus to include only those atoms and bonds you are working on: 1. Select the fragment or set of atoms or bonds. 2. Click Set Focus to Selection on the View Focus submenu of the View menu. Once you have set the view focus, the following things happen: • When building with the bond tools, Chem3D will resize and reposition the view so that all of the atoms in the view focus are visible. • As new atoms are added, they become part of the view focus. • When rotating, or resizing the view manually, the rotation or resize will be centered around the view focus. Setting Measurements You can set the following measurements using the Measurements submenu of the Structure menu: • Bond lengths • Bond angles • Dihedral angles • Close contacts NOTE: When you choose Measurement from the Structure menu, the display of the Set Measurement option will vary, depending on what you have selected. The grayed-out option says Set Measurement; when you select a bond, it says Set Bond Length, etc. When you use the Clean Up Structure command, the bond length and bond angle values are overridden by the standard measurements from the Optimal column of the Measurement table. These optimal values are the standard measurements in the Bond Stretching and Angle Bending parameter tables. For all other measurements, performing a ChemOffice 2005/Chem3D Building and Editing Models • 85 Setting Measurements
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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Chem3D Users Manual - CambridgeSoft

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