Chem3D 8.0 Manual - CambridgeSoft

AdministratorIf an atom can be assigned to more than one atomtype, atom types are assigned to atoms in thefollowing order:1. Atom types whose bound-to types are specifiedand are not the same as their rectification types.2. Atom types whose bound-to types are specifiedand are the same as their rectification types.3. Atom types whose bound-to types are notspecified.For example, in the model depicted above, O(4)could be one of several atom types. First, it could bean O Ether atom for which the bound-to type isunspecified (priority number 3, above).Alternatively, it could be an O Alcohol for which thebound-to type is the same as the rectification type, HAlcohol (priority number 2, above). A thirdpossibility is O Carboxyl, for which the bound-totype is C Carbonyl and the rectification type is HCarboxyl (priority number 1). Because thecharacteristic of a specified bound-to type which isnot the same as the rectification type (number 1 inthe priority list above) is given precedence over theother two possibilities, the O Carboxyl atom type isassigned to the oxygen atom.Defining Atom TypesIf you need to define atom types, whether to add tothe atom types table for building or to add to a fileformat interpreter for importing, here is the generalprocedure:To add or edit an atom type to the Atom Types table:1. From the View menu, choose Atom Types orAtom Types.TBL.The Table Editor opens and the Atom Typestable becomes the active window.2. From the Edit menu, choose New Atom Type.3. To edit an atom type, click in the cell that youwant to change and type new information.4. Enter the appropriate data in each field of thetable. Be sure that the name for the parameter isnot duplicated elsewhere in the table.5. From the File menu, choose Save, then chooseClose Window.You now can use the newly defined atom type.To define or edit an atom type in a file interpreter:1. In the Table Editor, choose the file interpreterthat you want to modify from the C3DFILTRdirectory.2. Follow the directions above for defining orediting atom types in the Atom Types table.A6 • CambridgeSoftDefining Atom Types