This menu contains commands that
Change Atom Colors: Change the color associated with an atomic number
Change Background Color: Change the color of the background
Update/Set External Paths: Update or set the path to an external program.
Added Parameters: Allows the addition of user defined constants
View Atom Types: View the atom types available in a force field
Edit Atom Types: Change the atom type assigned to a specific atom
Atom colors in Pcmodel are assigned by atomic number. Each element has an assigned color by default but this assignment can be changed and remembered. The Change Atom Color option brings up a dialog box with all the elements listed, a window for the color of the currently selected element, a button to change the color and a button to reset to default colors. First select and element to change then the Get New Color button. On all platforms this then brings up a standard color selection dialog. Select a new color and then OK to retun to the first dialog. Select the element again to see the new color in the color window. When done changing element colors just close the dialog. The new colors will remain in effect until the element color is changed.
The Change Background Color option brings up a standard color selection dialog. Select a new color and hit OK to dismiss the dialog and change the background color. This color is now the default background color for Pcmodel..
The paths to Mopac2012 and Gaussian can be viewed and set with this option. The Edit button brings up a standard file dialog to allow you to select the name of the program to run when the Mopac2012 and Gaussian options are selected from the Compute Menu.
The Added Parameters option allows the use of a file of user defined constants to be used in addition to or as replacements for the standard constants. The user is prompted for the name of the added constants file, which must use the same format as the standard constants file. PCMODEL checks as the added constants are read and replaces the standard constants if one exists or adds the new constant to the bottom of the parameter list if no previous constant has been defined. The added constants must be consistent with the force field used in the calculations. The Added Parameters remain in effect until the option is reselected (Toggle). The standard constants are read at program start and stored in memory and are not overwritten by the added parameters. The standard optimization procedure first copies the standard constants into the current parameter space, then applies added parameters and then proceeds with the calculation. So added parameters are used only when the Added Parameter option is selected.
This option lists all the atom types for a particular force field giving the atom type number and a short text description of the atom type.
This option gives the atom types of the currently selected atom. Use SELA to select an atom and then use the Edit Atom Types. A new dialog box is shown giving the Force Field, the atom type assigned to that atom in that Force Field and an edit box. Use the edit box to set a new atom type number in that force field to that atom only. The atom will no longer be retyped. If you are developing new atom types you must create the new atom type and all the associated data and add this to the standard parameter file for that force field before starting Pcmodel. The new atom type assigned to a specific atom can be written to a structure file in Pcmodel format for later use. The only means for getting new atom types into Pcmodel is to edit the standard parameter files.