VMD User's Guide

• add volumetric(molid, name, origin, xaxis, yaxis, zaxis, xsize, ysize, zsize, data):Add a volumetric data set to the given molecule. origin, xaxis, yaxis, andzaxis must be3-tuples specifying the center and scale of the data. xsize, ysize and zsize give the numberof elements along each dimension. data must be a Python list of the correct size as indicatedby the three sizes.• get filenames(molid):Returns a list of filenames that have been loaded into this molecule.• get filetypes(molid):• get databases(molid):• get accessions(molid):Returns a list of filetypes corresponding to get filenames.Returns a list of databases corresponding to get filenames.Returns a list of accessiosn corresponding to get filenames.• get remarks(molid):Returns a list of remarks corresponding to get filenames.• delframe(molid, beg=0, end=-1, skip=1): Delete frames from the specified molecule.Optional arguments beg, end, andskip may be specified with keywords; the default is todelete all coordinate frames.• dupframe(molid, frame):a new frame.Copy the coordinates from the given frame and append them as• numframes(molid):• get frame(molid):Return the number of coordinate frames in the specified molecule.Return the current coordinate frame for the specified molecule.• set frame(molid, frame):Set the current coordinate frames in the specified molecule.• numatoms(molid):Returns the number of atoms in the specified molecule.• ssrecalc(molid): Recalculate the secondary structure for the given molecule, using thecurrent set of coordinates.• name(molid):Returns the name of the given molecule.• rename(molid,newname):Rename the given molecule.• get top(molid):• set top(molid):Get/set the molid of the top molecule.• get periodic(molid, frame=-1):• set periodic(molid, frame=-1, a, b, c, alpha, beta, gamma): Get/set periodic imagesettings for the given molecule and timestep (frame). get periodic returns a dictionarywhose keys are a, b, c, alpha, beta, gamma. set periodic sets the corresponding values;negative values will be ignored.139