mol

Load, modify, or delete a molecule in VMD. In the following, molecule_number is a string describing which molecules are to be affected by the command. It is one of the following: all, top, active, inactive, displayed, on, off, fixed, free, or one of the unique integer ID codes assigned to the molecules when they are loaded (starting with 0). The codes (molIDs) are not reused after a molecule is deleted, so if you, for example, have three molecules loaded (numbered 0, 1, 2), delete molecule with molID equal to 0, and then load another molecule, the new molecule will have molID 3. Thus, the list of available molecule IDs becomes (1 2 3). The index of the molecule on this list is, among many other things, accessible through the molinfo command. In the above case, for example, molecule that was loaded the last has molID equal to 3, however, it is the third on the list of molecules, so it has the index equal to 2 (since we start countin from 0).

The molecule representations (views) are assigned integer number (starting with 0 for each molecule), which appear in the list on the Graphics form. The representations can be added, deleted or changed with the mol command. See also sections on molinfo command for more ways of retrieving information about the representations. See Chapter §  for information on how to use mol command to load user-defined graphics.

• < new | load > structure_file_type structure_file [coordinate_file_type coordinate_file] : Load a new molecule from filename(s) using the given format.
• urlload <file_type> <URL>: Load a molecule of file_type from a given URL address.
• pdbload <four_letter_accession_id>: ftp molecule from PDB. This command is deprecated; please use the following command instead: mol load webpdb <four_letter_accession_id>
• list: Print a one-line status summary for each molecule.
• list molecule_number: Print a one-line status summary for each molecule matching the molecule_number. If only one molecule matches the molecule_number, also print the representation status for this molecule, i.e., number of representations as well as the representation number, coloring method , representation style and the selection string for each of the representations.
• color coloring_method: Change the default atom coloring method setting.
• representation rep_style: Change the default rendering method setting.
• selection select_method: Change the default atom selection setting.
• modcolor rep_number molecule_number coloring_method: Change the current coloring method for the given representation in the specified molecule.
• modmaterial rep_number molecule_number material_name: Change the current material for the given representation in the specified molecule.
• modstyle rep_number molecule_number rep_style: Change the current rendering method (style) for the given representation in the specified molecule.
• modselect rep_number molecule_number select_method: Change the current selection for the given representation in the specified molecule.
• addrep molecule_number: Using the current default settings for the atom selection, coloring, and rendering methods, add a new representation to the specified molecule.
• delrep rep_number molecule_number: Deletes the given representation from the specified molecule.
• modrep rep_number molecule_number: Using the current default settings for the atom selection, coloring, and rendering methods, changes the given representation to the current defaults.
• delete molecule_number: Delete molecule(s).
• active molecule_number: Make molecule(s) active.
• inactive molecule_number: Make molecule(s) inactive.
• on molecule_number: Turn molecule(s) on (make drawn).
• off molecule_number : Turn molecule(s) off (hide).
• fix molecule_number: Fix molecule(s).
• free molecule_number: Unfix molecule(s).
• top molecule_number: Set the top molecule.
• cancel molecule_number: Cancel loading trajectories.
• ssrecalc molecule_number: Recalculate secondary structure based on the current set of coordinates.
• selupdate rep_number molecule_number boolean: Update the selection for the specified rep each time the frame changes.