VMD User's Guide

– ambient– specular– diffuse– shininess– opacity• delete name: Delete the given material.8.3.17 measureThe measure command supplies several algorithms for analyzing molecular structures. In thefollowing options, selection refers to an atom selection, as returned by the atomselect commanddescribed in section 8.3.2. The optional weight must be either none, an atom selection keywordsuch as mass, or a list of values, one for each atom in the selection, to be used as weights. If weightis missing or is none, then all weights are taken to be 1. When an atom selection keyword is used,the weights are taken from selection1.• avpos selection [first first] [last last] [stepstep]: Returns the average position of each ofthe selected atoms, for the selected frames. If no first, last, or step values are provided thecalculation will be done for all frames.• center selection [weight weight]: Returns the geometric center of atoms in selection usingthe given weight.• contacts cutoff selection1 [selection2]: Find all atoms in selection1 that are within cutoff ofany atom in selection2 and not bonded to it. If selection2 is omitted, it is taken to be thesame as selection1. selection2 and selection1 can either be from the same of from differentmolecules. Returns two lists of atom indices, the first containing the first index of each pair(taken from selection1) and the second containing the second index (taken from selection2).Note that the index is the global index of the atom with respect to its parent molecule, asopposed to the index within the given atom selection that contains it.• fit selection1 selection2 [weight weight]: Returns a 4x4 transformation matrix which, whenapplied to the atoms in selection1, minimizes the weighted RMSD between selection1 andselection2. See section 11.4.2 for more on RMSD alignment.• gofr selection1 selection2 [delta value] [rmaxvalue] [usepbcboolean] [selupdateboolean][first value] [last value] [stepvalue]: Calculates the atomic radial pair distribution functiong(r) and the number integral ∫ r0 ρg(r)r2 dr for all pairs of atoms in the two selections. Bothselections have to reference the same molecule and may be identical. In case one of theselections resolves to an empty list for a given time step, and empty array is added to thehistograms. The command returns a list of five lists containing r, g(r), ∫ r0 ρg(r)r2 dr, theunnormalized histogram, and a list of frame counters containing currently 3 elements: totalnumber of frames processed, the number of skipped frames and the number of frames handledwith the orthogonal cell algorithm (Further algorithm and corresponding list entris will beadded in the future). With the optional arguments delta (default 0.1) and rmax (default10.0) one can set the resolution and the maximum r value. With the usepbc flag processing103