VMD User's Guide

8.3.33 vmdinfo(Tcl) Returns information about this version of VMD.• version: Returns the version number;• versionmsg: Full information about this version;• authors: List of authors;• arch: architecture type (in case you couldn’t tell);• options: options used to compile VMD;• www: VMD home page;• wwwhelp: VMD help page.This function is available without Tcl and the information is displayed to the screen.8.3.34 volmapThe volmap command creates volumetric maps (3D grids containing a value at each grid point)based on the molecular data, which can then be visualized in VMD using the Isosurface andVolumeSlice representations or using the Volume coloring mode. Also note that the VolMap plugin,accessible from the VMD Extension menu, provides a graphical front-end to many of the volmapcommand’s capabilities.To create a volumetric map, the volmap command is run in the following way, where the atomselection specifies the atoms and molecule to include in the calculation, and where the maptypespecifies the type of volumetric data to create:volmap [optional arguments]For example, to create a mass density map with a cell side of 0.5 Å, averaged over all frames ofthe top molecule, and add the volumetric data to the top molecule, on would use:volmap [atomselect top "all"] density -res 0.5 -weight mass -allframes \-combine avg -mol topThe various volumetric data map types currently supported by volmap are listed as follows.Please note that when a map type description refers to an atoms radius or beta field, etc., thatthese values will be read directly from VMD’s associated fields for that atom. In certain cases, youmay want to adjust the atom selections fields (such as radius, beta, etc.) before performing thevolmap analysis.• density: creates a map of the weighted atomic density at each gridpoint. This is doneby replacing each atom in the selection with a normalized gaussian distribution of width(standard deviation) equal to its atomic radius. The gaussian distribution for each atom isthen weighted using an optional weight (see the -weight argument), and defaults to a weightof one (i.e, the number density). The various gaussians are then additively distributed on agrid.115