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Administrator change a property. By changing some property of a lower level object, you can better visualize the part of the model you want to study. Use the Model Explorer to: • Define objects. • Add objects to groups. • Rename objects. • Delete objects, with or without their contents. The display properties of objects you can alter include: • Changing the display mode. • Showing or hiding. • Changing the color. At the atom level, you can display or hide: • Atom spheres • Atom dots • Element symbols • Serial numbers Model Explorer Objects The Model Explorer objects are: • Fragments • Chains • Groups • Atoms • Bonds • Solvents • Backbone The Fragment object represents the highest level segment (“parent”) of a model. Fragments represent separate parts of the model, that is, if you start at an atom in one fragment, you cannot trace through a series of bonds that connect to an atom in another fragment. If you create a bond between two such atoms, Chem3D will collapse the hierarchical structure to create one fragment. Fragment objects typically consist of chains and groups, but may also contain individual atoms and bonds. In Chem3D, chains and groups are functionally identical. Chains are special groups found in PDB files. If you rename a group as a chain, or vice versa, the icon will change. This is also the reason that only the work “Group” is used in the menus. All Group commands also apply to chains. Group objects can consist of other groups, atoms and bonds. Chem3D does not limit a group to contiguous atoms and bonds, though this is the logical definition. Bond objects do not appear by default in the Model Explorer. If you want to display bonds, select Show Bonds in the GUI tab of the Chem3D Preferences dialog box. The Solvent object is a special group containing all of the solvent molecules in the model. The individual molecules appear as “child” groups within the Solvent object. A Solvent object should not be child of any other object. NOTE: When importing PDB models, solvents will sometimes show up in chains. While this is incorrect, Chem3D preserves this structure in order to be able to save the PDB file again. The Backbone object is a display feature that allows you to show the carbon-nitrogen backbone structure of a protein. It appears in the Model Explorer as a separate object with no children. The atoms and bonds that make up the backbone belong to other chains and groups, but are also virtual children of the Backbone object. This allows you to select display properties for the backbone that override the display properties of the chains and groups above them in the hierarchy. To display the Model Explorer: • From the View menu choose Model Explorer. 108•Inspecting Models <strong>CambridgeSoft</strong> Working With the Model Explorer
The Model Explorer window appears along the left side of the model. When you change an object property, the object icon changes to green. When you hide an object, the icon changes to red. Objects with default properties have a blue icon. hidden changed Creating Groups To view or change a property in a model: 1. Select the object (fragment, group, or atom) you wish to change. TIP: To select multiple objects, use Shift+click if they are contiguous or Ctrl+click if they are not. 2. Right-click, select the appropriate submenu, and choose a command. Some models, PDB proteins for example, have group information incorporated in the file. For other models you will need to define the groups. To do this in the Model Explorer: 1. Holding down the Ctrl key, select the atoms in the group. 2. Choose New Group from the Context- Sensitive menu. The group is created with the default name selected. 3. Rename the group by typing a new name. Adding to Groups You can add lower level objects to an existing group, or combine groups to form new groups. <strong>ChemOffice</strong> 2005/Chem3D Inspecting Models • 109 Working With the Model Explorer
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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 Atom Properties . . .
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Administrator Deleting a Field Type
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Administrator Example 2. . . . . .
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Administrator 26 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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Administrator To use the same text
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CAMBRIDGESOFT ChemOffice Desktop to
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CONSULTING & Consulting & Services
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CS Software Problem Report For fast
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