VMD User's Guide

• Representation Method – The surface can optionally be drawn using lines rather than solidtrianglesThis surface is rather slow in both generation and display for systems over several hundredatoms. The SURF calculation is quite exact and will show complete detail even when it isn’tneeded. The use of disk space as an interprocess communications medium takes up about half ofthe run time.There is an environment variable [§ 12.2] which can affect the Surf display option:• SURF BIN – location of the SURF binary (defaults to SURF $ARCH as defined in the vmd startupscript)A helpful trick when constructing surfaces is to use the Apply Changes Automatically togglebutton on the graphics form wisely. That is, since surfaces often take a long time to build, changingviewing parameters such as the probe radius can cause long delays. By default, each time you hitthe probe radius button, VMD rebuilds the surface. If you want to reduce or enlarge the proberadius by several increments, then you would end up rebuilding the surface multiple times. Bytoggling the afore-mentioned button, you can force VMD to update on your command only. Thistrick is sometimes helpful with other representations as well.For a much faster surface rendering method, see the description of ‘MSMS’ [§ 5.1.16].5.1.16 MSMSAnother molecular surface renderer is ‘MSMS’, a program written by Michael Sanner of Olsen’s labat Scripps. This program is much faster than Surf, and can be a better choice depending on how it isused. See the web page http://www.scripps.edu/pub/olson-web/people/sanner/html/msms home.htmlfor more details. Available options include• Which Atoms – should the surface be of the selection (0) or of the contribution of this selectionto the surface of all the atoms? (1)• Sample Density – triangle density on the surface (typical values are 1.0 for molecules withmore than one thousand atoms and 3.0 for smaller molecules)• Probe Radius – Probe radius used to construct the molecular surface• Representation Method – The surface can optionally be drawn using lines rather than solidtrianglesThere is an environment variable [§ 12.2] which can affect the MSMS display option:• MSMSSERVER – location of the MSMS binary (defaults to msms whichisassumedtobeintheuser’s path) On Windows machines, sets this as a systemwide environment variable in theenvironment variables window found in the system properties control panel.5.1.17 VolumeSliceThe ‘VolumeSlice’ representation draws a texture mapped two-dimensional slice from a volumetricdata set already loaded into VMD using the mol volume [§ 8.3.19] text command, or by othermeans. The colors span the scalar value range of the data set, with red indicating low values and63