ANNOUNCE: VMD version 1.1 is now available
dalke at ks.uiuc.edu
Thu May 16 22:55:04 EST 1996
Announcing version 1.1 release of VMD
The Theoretical Biophysics group at the University of Illinois and the
Beckman Institute would like to announce the availability version 1.1
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 a precompiled binary for
Silicon Graphics workstations running version 5 or later of the IRIX
operating system. The postscript documentation (still being updated
to include the new features in version 1.1) 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 such as Mosaic or Netscape.
New in this version
This biggest improvement in version 1.1 is the development of
scripting functions for molecular analysis and the 3D display of the
results. These include:
* Querying the internal VMD data base for information about
a atom or set of atoms
* Built-in functions for computing the center of mass,
radius of gyration, etc. of an atom selection
* Complete script control over atom position information
* Adding and modifying graphical items (lines, spheres, etc.)
in the display window to build user-defined scenes
* Best (RMSD) fit alignment of molecules using the Kabsch method
* Addition of Tcl-X and Tcl-DP
* More control over internal VMD parameters
* Vector and matrix routines for coordinate analysis
Other improvements include:
* Mouse controls for modifying the coordinates of an atom,
residue or fragment (useful for structure building)
* New rendering styles including cartoon
* Orthographic perspective mode
* New atom selection methods
* Automatic secondary stucture determination (using STRIDE)
* Ability to add forces to a molecular dynamics simulation
* Support for the Radiance and ART ray tracers
* Reduced levels of detail for faster visualization of
and, of course, many bug fixes.
============== Basic information about VMD ===================
A more complete description of VMD is available via the VMD WWW home
The software itself is available via anonymous ftp in the directory:
(please see the README file in this directory for the latest version
Email questions to vmd at ks.uiuc.edu.
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
The program has many features, which include:
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 more).
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,
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 structure.
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' environment.
VMD runs on Silicon Graphics workstations and may be compiled for
HP-UX workstations if the NPGL library (a commercial port of the SGI
GL library, available from Portable Graphics, Inc.) is available on
your system, or to IBM 6000s with GL. Two versions of the
distribution are available, one including the complete VMD source
code, and one which just includes a precompiled VMD executable for SGI
IRIX version 5.x.
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 and the
National Science Foundation.
vmd at ks.uiuc.edu
May 15, 1996
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