This menu contains the following commands:
Select Molecule: Set the molecule as selected so that it may be manipulated with the standard mouse controls.
Clear Selected Molecule: Deselect the currently selected molecule.
Connect Molecules: Connect two molecules using the selected hydrogen atoms in each molecule.
Find All Molecules: Loop through the atoms list and group all connected atoms into a molecule
Delete Molecule: Delete a selected molecule
Group Molecule Numbers: Assign molecules with the same formula and molecule weight to the same molecule number.
All atoms are assigned a molecule number.. By default the first structure read into PCMODEL using the OPEN command, or any structure drawn in the Structure window is initially assigned to molecule number zero (0). Several molecules may be drawn in the Structure window, but they all belong to molecule zero and all will be moved, erased or minimized together. In order to manipulate the structures individually it is necessary to identify them as separate molecules using the Find All Molecules command and then Select Molecule. Whenever a new molecule is read into Pcmodel with the File Open command and the old structure(s) are kept the new structure is given a new molecule number. By default the current Selected Molecule is set to -1. Using the Select Molecule command sets this variable to the molecule number of the selected molecule while Clear Selected Molecule sets the variable back to -1. When there is no selected molecule the mouse controls for rotation and translation apply to all atoms. When there is a selected molecule the mouse control apply only to that molecule.
Selecting a molecule can be done in two ways. The first is to select any atom in a molecule using SELA and then the Select Molecule command. All the atoms in the molecule will be highlighted. The second method is to double click on any atom in a molecule. You can tell the molecule is selected because all the atoms in the molecule will be highlighted. To change from one selected molecule to a different molecule either double click on an atom in the new molecule or use SELA to select an atom in the new molecule and use the Select Molecule command. The selected molecule remains in effect until reset with the Clear Molecule command.
Reset the selected molecule variable to -1 and remove the highlighting of the atoms of the selected molecule.
The Connect command connects two structures. First, SELECT the two hydrogens to be removed to make the new bond (using the SELA button in the TOOLS men). The hydrogens will be removed and a new bond will be drawn between the two heavy atoms to which the hydrogens were attached.
Erase all molecule information and then loop through all the atoms grouping those that are attached into molecules. Starting with the first atom Pcmodel runs through the lists of bonds to find all the atoms attached to the first atom and then repeats the search on the attached atoms. The search proceeds until no new attachments can be found. All of found atoms are assigned the same molecule number. If there are still unassigned atoms the procedure is repeated starting from the first unassigned atom and continues until all atoms are assigned to a molecule. A simple example could be a PDB file containing a protein, several copies of a bound small molecule and many copies of water. Find All Molecule would assign the protein one molecule number, each of the bound small molecules would get a different molecule number and each water molecule would have a different molecule number. Each molecule could then be manipulated separately. See the Group Molecule Numbers command below.
If there is an atom selected (using SELA) then that molecule will be deleted. If no atoms are selected then Pcmodel checks the total number of molecules. If less than 35 a scrolling list is shown and you may select the molecule to delete. If greater then 35 molecules then you will be asked if you want to Group Molecule Number first to make the process more efficient. If you say no then the scrolling list of all molecules is presented. If you have used the Group Molecule Numbers command then the scrolling list will have the Molecule Formula, Molecular Weight and the number of copies of each molecule.
This command calculates the molecular formula and weight of all the molecules and then combines all those molecules that have the same formula and weight into a group with the same molecule number. From the example above – after the molecules are group both small, bound molecules would have the same molecule number and all the waters would have the same molecule number. This makes it much easier to delete all the water molecules at once. You can always recover the individual molecule numbers by running the Find All Molecule command again.