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.

• new [ filename ] [ options ]:
• addfile < filename > [ options ]:

  mol new is used to create a new molecule from a file; if the optional filename parameter is omitted, a plain, ``blank'' molecule is created with no atoms (this can be used to create a canvas for drawing user-defined geometry). mol addfile is like mol new except that the structure and coordinate data are loaded into the top molecule (whichever molecule was loaded last) instead of creating a new one. Both mol new and mol addfile accept the following set of options:

  • type <type>: Specifies the file type (psf, pdb, etc.) If this option is omitted, the filename extension is used to guess the filetype; otherwise, it overrides what would be guessed from the filename.
  • first <frame>:
  • last <frame>:
  • step <frame>: For files containing coordinate frames , specifies which frames to load. Frames are indexed starting at 0. A step of 1 means all frames in the range will be loaded; a step of 2 means load every other frame.
  • waitfor <frames>: For files containing coordinate frames , specifies how many frames to load before returning; the default is 1. If frames is less than the number of frames in the file, the rest of the frames will be loaded in the background on subsequent VMD display updates. If frames is -1 or all, then all frames in all files still in progress will be loaded at once before the command returns. Frames loaded this way will load faster than if they are loaded in the background. If files are still being loaded in the background when the addfile command is issued, frames from the files in progress will be loaded first.
  • volsets <set ids>: For files containing volumetric data, specifies which data sets to load. <set ids> should be a list of zero-based indices.
  • molid: For addfile only. The molecule id of the molecule into which the file should be loaded may be specified. It must be the last option specified. If omitted, the default is the top molecule.

• load structure_file_type structure_file [coordinate_file_type coordinate_file] : Load a new molecule from filename(s) using the given format. If an additional coordinate file is specified, load this file as well. New in VMD 1.8: All frames from the coordinate file will be loaded before the command returns. If this is not desirable, use the animate read command for more fine-grained control over how coordinate files are loaded. Previous version of VMD loaded only one frame before returning. The function will return the id of the newly created molecule, or return an error if unsuccessful.

• urlload <file_type> <URL>: Load a molecule of file_type from a given URL address. Return the id of the newly created molecule, or an error if unsuccessful.

• pdbload <four_letter_accession_id>: Retrieve the PDB file with the specified accession code from the RCSB web site. Returns the id of the newly created molecule, or an error if unsuccessful.

• 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.
• clipplane center clipplane_id rep_number molecule_number [ vector ]
• clipplane color clipplane_id rep_number molecule_number [ vector ]
• clipplane normal clipplane_id rep_number molecule_number [ vector ]
• clipplane status clipplane_id rep_number molecule_number [ boolean ]
• 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
• rename molecule_number newname: Rename the specified molecule.
• repname molecule_number rep_number: Returns the name of the given rep. This name is guaranteed to be unique for all reps in the molecule, and will stay with the rep even if the rep_number changes.
• repindex molecule_number name: Return the rep_number for the rep with the given name, or -1 if no rep with that name exists in that molecule.
• selupdate rep_number molecule_number [onoff]: Update the selection for the specified rep each time the molecule's timestep changes. If onoff is not specified, returns the current update state.
• colupdate rep_number molecule_number [onoff]: Update the calculated color for the specified rep each time the molecule's timestep changes. If onoff is not specified, returns the current update state.
• drawframes molecule_number rep_number [frame_specification]: Draw multiple trajectory frames or coordinate sets simultaneously. This setting allows the user to select one or more ranges of frames to display simultaneously. The frame specification takes one of the following forms now, frame_number, start:end, or start:step:end. If the frame_specification is not specified, the command returns the currently active frame selection text.
• smoothrep molecule_number rep_number [n]: Get/set the window size for on-the-fly smoothing of trajectories. Instead of drawing the specified rep from the current coordinates, VMD will calculate the average of the coordinates from the $n$ previous and subsequent timesteps. If $n$ is zero then no smoothing is performed. Note that this smoothing does not affect any label measurements, and does not change the values of the coordinates returned by atom selections or written to files; it only affects how the rep is drawn. Smoothing can be especially useful in visualizing rapidly fluctuating molecules or making movies.
• scaleminmax molecule_number rep_number [min max | auto]: Get/set the color scale range for this rep. Normally the color scale is automatically scaled to the minimum and maximum of the corresponding range of data. This command overrides the autoscaled values with the values you specify. Omit the min and max arguments to get the current values. Use ``auto" instead of a min and max to rescale the color scale to the maximum range again.
• showrep molecule_number rep_number [on | off]: Get/set whether the given rep is shown or hidden. Hidden reps cannot be picked and do not show any graphics.
• volume molecule_number <volumeset_name> <Origin> <a> <b> <c> #a #b #c <Data> Add a volumetric data set to the current molecule. Origin, a, b, and c are vectors setting the origin and the three cell vectors. #a, #b, and #c are the number of grid points in the respective cell vector directions and finally the data has to be provided as one list with the data following the grid points along the c-axis fastest, then the b-axis and finally the a-axis.