ANNOUNCE: VMD 1.2b1 now available
dalke at ks.uiuc.edu
Tue Mar 25 03:35:21 EST 1997
(The following announcement should be of interest to subscribers
if this group as VMD can read XPLOR PDB and PSF files as well
as animate DCD trajectories.)
Announcing version 1.2b1 release of VMD
The Theoretical Biophysics group at the University of
Illinois and the Beckman Institute would like to announce
the availability version 1.2b1 of the program VMD, a package
for the vizualization and analysis of biomolecular systems.
This software is being made available to the structural
biology research community free of charge, and includes the
source code for VMD, documentation, and precompiled binaries
for SGIs, HPs, and Linux. The postscript documentation
(still being updated) includes an installation guide, a
users guide, and a programmers guide for interested
researchers. VMD also provides on-line help through the use
of an external HTML viewer.
A full description of VMD is available via the VMD WWW home page:
New in this version
o This biggest improvement in version 1.2b1 support for
platforms other than GL-based SGIs. In addition to the full
source and SGI binary distributions, VMD is now available
for HP-UX (tested under 9 and 10) and Linux. Ports to other
platforms, most notably AIX, will be available soon.
o Greatly enhanced Tcl scripting commands for performing
molecular analysis, writing scripts, developing tutorials,
o New rendering styles, a fast (and cheap) solvent
accessible surface and C-alpha and P trace method, and
improvements to the existing styles.
o New output renderer formats: Postscript, VRML and STL (a
o Support for Amber structure and animation file formats
And of course, many bug fixes.
============= Basic information about VMD =================
VMD is designed for the visualization and analysis of
biological systems such as proteins, nucleic acids, lipid
bilayer assemblies, etc. It may be used to view more
general molecules, as VMD can read standard Protein Data
Bank (PDB) files and display the contained structure. VMD
provides a wide variety of methods for rendering and
coloring a molecule: simple points and lines, CPK spheres
and cylinders, licorice bonds, backbone tubes and ribbons,
cartoon drawings, and others. VMD can be used to animate
and analyze the trajectory of a molecular dynamics (MD)
simulation. In particular, VMD can act as a graphical front
end for an external MD program by displaying and animating a
molecule undergoing simulation on a remote computer.
The program has many features, which include:
o No limits on the number of molecules, atoms, residues or
number of animation frames, excepting available memory.
o Many molecular rendering and coloring methods.
o Stereo display capability.
o Extensive atom selection syntax for choosing subsets of atoms for
display (includes boolean operators, regular expressions, and
o Integration with the program 'Babel' which allows VMD to read many
molecular data file formats. Even without the use of Babel,
VMD can read PDB files, as well as CHARMM- and X-PLOR compatible
binary DCD files and X-PLOR compatible PSF files.
o Ability to write the current image to a file which may be
processed by a number of popular raytracing and image rendering
packages, including POV-Ray, Rayshade, Raster3D, and Radiance.
o Extensive graphical and text-based user interfaces, which use the
Tcl package to provide full scripting capabilities.
o Extensions to the Tcl language which enable researchers to write
their own routines for molecular analysis
o Modular, extensible source code using an object-oriented design in
C++, with a programmers guide describing the source code
o Integration with the program NAMD, a fast, parallel, and scalable
molecular dynamics program developed in conjunction with VMD
in the Theoretical Biophysics Group at the University of Illinois.
See the NAMD WWW home page for more info:
VMD can be used to set up and concurrently display a MD simulation
using NAMD. The two programs, along with the intermediary
communcations package (called MDComm) constitute the 'MDScope'
The software is available via anonymous ftp in the directory:
The filenames of the different distributions are:
The complete source:
Precompiled binaries for different platforms
Works for IRIX 5.x and 6.x using GL
Works for HP-UX 9 and HP-UX 10 using Mesa emulated OpenGL
Tested under RedHat with 1.2.13 and 2.0.27 kernals, uses Mesa
Please email any questions to vmd at ks.uiuc.edu.
VMD, NAMD, and the entire MDScope environment are part of
an ongoing project within the Theoretical Biophysics group
to help provide free, effective tools for molecular dynamics
studies in structural biology. For more information, see
http://www.ks.uiuc.edu/Research/MDScope/. This project is
funded by the National Institutes of Health (grant number
PHS 5 P41 RR05969-04) and the National Science Foundation
(grant number BIR-9318159).
vmd at ks.uiuc.edu
March 22, 1997
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