VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 22 2002 - 15:25:18 CST

Dear VMD-L,
  I've just made two new Tcl scripts available for people
to try out. They are both related to loading volumetric
data into VMD. They both require that you be using
VMD 1.7.1 or subsequent versions. Both scripts load a volume set
and add it to the "top" molecule in VMD, for use with the
"Volume Slice" and "Isosurface" representations in VMD 1.7.1.

See the "volumetric data scripts" page on the VMD site for these
scripts and others:
  http://www.ks.uiuc.edu/Research/vmd/script_library/volumetric.html

Note: The "VolumeSlice" representation is currently only available
      on machines that have support for 3-D texturing, and OpenGL 1.2.
      We expect to add support for older machines and those that lack
      the 3-D texturing capability in VMD 1.8

Here are the details of the two scripts:
  "readedm" - reads X-PLOR ASCII Electron Density Map files into VMD.
              We've tested it with both orthogonal and non-orthogonal
              cells, and we think it is correct in both cases. There may
              be minor variations of the file format that we haven't seen
              yet, so let us know if you have trouble loading any EDM files
              that you think should work with this script. This script
              should be a fairly decent starting point for those people
              that want to write loader scripts for the myriad of other
              kinds of volumetric data out there.

 "readcube" - This script was written by Francesco Luigi Gervasio,
              with some minor improvements I made after reading more
              about the "cube" format at the Gaussian web site. This
              script works with ASCII cube files, and seems to work ok
              for orthogonal unit cells, but still needs work in order to
              handle all cases correctly. If you have comments, improvements,
              or bug fixes, please let us know. In the mean time, I'm going
              to try and take our work from the "readedm" script and its
              code for non-orthogonal cells, and merge it into this script.

Please let us know if you have questions about how to load volume data
with these scripts, or if you need help using the "VolumeSlice" or
"Isosurface" representations in VMD.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078