VMD User's Guide

• add(name=None, copy=None): Create a new material with the given name. Optionally,copy the properties from material copy into the new material. If no name is given, a new onewill be provided.• delete(name):Delete the material with the given name.• rename(oldname, newname):must not yet be used.Rename the material with the given name. The new name• change(name, ambient, specular, diffuse, shininess, opacity): Change one or moreof the material settings for the material with the given name. Keyword arguments may beused to specify each property.9.5.9 moleculePython operations available from the molecule module, used to load molecules and change theirrepresentations.• num():Returns the number of loaded molecules.• listall():Returns the molid’s of the all the loaded molecules.• exists(molid):Returns true if the molid corresponds to an existing molecule.• new(name):Creates a new empty molecule with the given name and returns its id.• load(structure, sfname, coor, cfname): Load a molecule with structure type structureand filename sfname. Additionally, a separate coordinate file may be provided, of type coorand name cfname. New in VMD 1.8: All frames from cfname will be processed before thefunction returns. If successful, the function will return the id of the new molecule.>>> load(’pdb’,’alanin.’pdb’)>>> load(’psf’,’alanin.psf’,’dcd’,’alanin.dcd’)• cancel(molid):• delete(molid):Cancel loading of coordinates file for the given molecule.Delete the specified molecule.• read(molid, type, filename, beg = 0, end = -1, skip = 1, waitfor = 1, volsets= [1]):• write(molid, type, filename, beg = 0, end = -1, skip = 1, waitfor = 1): Reador write a file to/from the specified molecule. For reading, if molid is -1, a new moleculewill be created. Optional arguments beg, end, andskip may be specified with keywords;the default is to load/save all coordinate frames. New in VMD 1.8: The waitfor optionwill cause VMD to process the specified number of frames before returning. If waitfor isnegative, all frames from the file will be processed before the function returns. For readingfiles containing volumetric datasets, set the volsets parameter to a list of set id’s, startingfrom 0, to specify which datasets to load.138