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