ANNOUNCE: VMD 1.2b1 now available

Andrew Dalke dalke at ks.uiuc.edu
Sun Apr 6 10:51:24 EST 1997


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:
        http://www.ks.uiuc.edu/Research/vmd/


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,
     etc.

 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
     stereo-lithography format)

 o Support for Amber structure and animation file formats

  And of course, many bug fixes.

 =============   Basic information about VMD   =================

Features
--------

  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  
      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, 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:  
             http://www.ks.uiuc.edu/Research/namd

      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.  

Availability
------------

The software is available via anonymous ftp in the directory:
        ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd/

The filenames of the different distributions are:
  The complete source:
    vmd-1.2b1.all.tar.gz

  Precompiled binaries for different platforms
    vmd-1.2b1.bin.IRIX5.tar.gz
	Works for IRIX 5.x and 6.x using GL
    vmd-1.2b1.bin.HPUX9.tar.gz
	Works for HP-UX 9 and HP-UX 10 using Mesa emulated OpenGL
    vmd-1.2b1.bin.LINUX.tar.gz
	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).

						Andrew Dalke
						vmd at ks.uiuc.edu
						March 22, 1997




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