Chapter 11 Substr Menu
This menu contains the following commands:
Read Read a structure file and label the structure as a substructure.
Create Label the selected structure as a substructure
Move Moves the selected substructure.
Connect Connect two structures.
Erase Removes the selected substructure from existence.
Show Dummy Display any dummy atoms in current structures.
Don't minimize Marks the selected substructure so that it will not be minimized in a molecular mechanics calculation.
Substructures are a method for naming and manipulating individual molecules. By default any structure read into PCMODEL using the OPEN command, or any structure drawn in the Structure window is initally assigned to substructure number zero. Several molecules may be drawn in the Structure window, but they all belong to substructure zero and all will be moved, erased or minimized together. In order to manipulate the structures individually it is necessary to mark them as substructures. The commands available in the Substructure Menu provide all the facilities necessary for handling substructures.
The READ command reads a structure file into PCMODEL, marks it with a unique substructure number and displays it to the right of the current structure. The current structure is not erased. A file open dialog box is used for obtaining the filename, filetype and path (see the FILE OPEN command for a detailed description of this dialog box). Up to thirty two substructures may be created at one time in PCMODEL.
The CREATE command marks a structure present in the Structure window as a substructure. Before choosing CREATE, at least one atom in the structure must have been marked with the SELECT button from the TOOLS menu. When the CREATE command is chosen, a dialog box appears requesting a name for the substructure. This name is associated with the substructure and can be used with the MOVE, ERASE, HIDE and DON'T MINIMIZE commands.
The MOVE command allows one substructure to be translated and or rotated with respect to all the other structures. There are several methods for selecting the substructure to move. One method is to use the SELECT button on the TOOLS menu to mark an atom in the substruture to be moved before chosing MOVE. Alternatively, if no atoms have been selected when the MOVE command is chosen, a dialog box will be presented listing all substructures by name, and the substructure to be moved can be chosen by selecting its name from the list with either the left mouse button or the up/down arrow keys. After a substructure has been selected, click on OK, and the Control Panel dialog box will appear. The translate and rotate controls will now only work on the selected substructure. Rotation will be about the center of the selected substructure.
To change the substructure being moved, simply select an atom in another substructure. The Control Panel controls will now operate on that substructure. Complex docking can be accomplished by translation and rotation of selected substructures. To rotate the entire collection of molecules as a unit it is necessary to Exit the Control Panel dialog box, and then chose the CONTROL_PANEL option from the VIEW menu.
The Connect command connects two structures. First, SELECT the two hydrogens to be removed to make the new bond (using the SELECT button in the TOOLS men). The hydrogens will be removed and a new bond will be drawn between the two heavy atoms that the hydrogens were attached to. Please see Chapter 3, Tutorials, for a step by step description of connecting two molecules.
The ERASE command allows a substructure to be erased (deleted from existance). As with SUBST MOVE, any atom in the substructure to be deleted may be SELECTed before chosing ERASE, or if none are selected a dialog box will list the possible substructures. There is no prompt for confirmation. Once the structure is deleted it can not be recovered.
The SHOW DUMMY commands redraws the structure with all dummy atoms (atom type 60 in MMX) shown with gray dots over the atom. Dummy atoms can be placed in a structure using the Dummy Atom type from the periodic table. Dummy atoms have the same properties as hydrogens and can thus be minimized, but they are not removed by HAD. The main purpose of Dummy atoms is to serve as place holders for points of connection while building polymers or other large structures. See the Tutorial Chapter of the use of dummy atoms in building poly-stryene.
The DON'T MINIMIZE command marks a substructure so that it will be ignored during an energy minimization. This is a useful procedure when studying interactions between surfaces and molecules, in which the interactions between the surface and the molecules are of interest, but minimizing the surface would not be practical. This allows building surfaces that are only two or three atoms deep, and thus would not maintain their geometry if minimized, reading the surfaces into PCMODEL and then studing the interaction of these surfaces with various molecules. As with SUBST MOVE, any atom in the substructure to be deleted may be SELECTed before chosing DON'T MINIMIZE, or if none are selected a dialog box will list the possible substructures.