VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 24 2001 - 10:03:39 CDT

        VMD "Visual Molecular Dynamics" 1.6.1 Announcement
        --------------------------------------------------
The Theoretical Biophysics group at the Beckman Institute For Advanced
Science and Technology, the University of Illinois (U-C), is proud to
announce the public release of VMD 1.6.1. VMD is a package for the
visualization and analysis of biomolecular systems. This software is
distributed free of charge and includes source code, documentation,
and precompiled binaries for Compaq, IBM, HP, Linux, MacOS-X, Sun,
and SGI Unix systems, as well as Microsoft Windows 95/98/ME/NT/2K.
The VMD documentation 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. VMD development is
supported by the NIH National Center for Research Resources.

A full description of VMD is available via the VMD WWW home page:
        http://www.ks.uiuc.edu/Research/vmd/

The authors request that any published work which utilizes VMD includes
a reference to the VMD web page and/or the following reference:

  Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular
  Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.

The Theoretical Biophysics group encourages VMD users to be closely
involved in the development process through reporting bugs, contributing
fixes, periodical surveys and via other means.

We are eager to hear from you, and thank you for using our software!

                                                John Stone
                                                vmd_at_ks.uiuc.edu
                                                April 22, 2001

                       README file for VMD 1.6.1
---------------------------------------------------------------------------

What is VMD? See also http://www.ks.uiuc.edu/Research/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, 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 limit on the number of molecules, atoms, residues or
    number of animation frames, except available memory.

  o Many molecular rendering and coloring methods.

  o Stereoscopic display capability using Red/Blue or LCD shutter glasses.

  o Extensive atom selection syntax for choosing subsets of atoms for
    display (includes boolean operators, regular expressions, and more).

  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, Radiance, Raster3D, Rayshade,
    and Tachyon.

  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 Extensive graphical and text-based user interfaces, which use the
    Tcl package to provide full scripting capabilities.

  o Extensions to the Tcl and Python languages 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 programmer's guide outlining 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 information:
      http://www.ks.uiuc.edu/Research/namd

  o VMD can be used to interactively display and control an MD simulation
    using NAMD or Protomol.

  o Integration with the BioCoRE collaborative research environment.
    VMD can "publish" molecular graphics scripts to BioCoRE, so that
    BioCoRE collaborators can work together over the internet.
    See the BioCoRE WWW home page for more information:
      http://www.ks.uiuc.edu/Research/biocore

What's new in VMD 1.6.1?
------------------------
  New Features
    o Some builds of VMD now support multiprocessor acceleration and
      multithreading for improved I/O performance even on uniprocessors.
    o Multithreaded IMD socket I/O for improved performance on high latency
      networks and with slow simulations.
    o Ported VMD to MacOS-X using Mesa, requires XFree86 be installed.
    o Support for 64-bit versions of VMD on IRIX 6.x and Solaris 2.x,
      using R10000 class SGI CPUs, and UltraSPARC class Sun CPUs.
      The 64-bit versions are capable of working with files larger than
      2GB, and can use more than 4GB of main memory if necessary.
    o New "getbonds" and "setbonds" commands for Tcl and Python
      atom selections. Replaces older "bond" command.
    o New real-time implementation of anaglyph (red/blue) stereo for
      people without LCD glasses, but with quad-buffered stereo hardware
      on their machine.
    o New atom selection keyword 'exwithin', eliminates need for a commonly
      used complex combination of atom selections '(within 3 of X) and not X'.
    o Works with BioCoRE. VMD can now "publish" configuration files to
      a BioCoRE notebook, such that collaborators can work together on VMD
      visualizations, using BioCoRE as their common workplace.
 
  General Improvements and Bug Fixes
    o Tcl "atomselect get" speed increased by 10-30x for large molecules for
      numeric selections. String-based selections slightly slower, but
      a good improvement for the common performance intensive use-cases.
    o Increased speed of "lines" representation drawing and animation by
      a factor of 3, allowing interactive rotation of huge systems in lines
      mode (4 million atom water box at 2 seconds per frame.)
    o Significant improvements in responsiveness in the the graphics form
      "atom name lists" for large molecules with hundreds of thousands of
      atoms. Very large name lists now display 10 to 30 times faster.
    o Increased the number of colors in the color scale map from 16 to 1024.
    o Significant updates to Python callback mechanism.
    o Fixed a minor EOF failure in G96 file reader
    o Built with FLTK 1.0.10 on all platforms.
    o Fixed PRs (bugs): 134, 136, 139, 140, 141, 145, 146,
                        148, 150, 151, 152, 153

  User Interface Changes
    o The rmsd fit routines can be brought up without needing to source
      a fully qualified pathname in the VMD installation directory
    o Updated the "Sim" form to improve the IMD interface

  User Documentation Updates
    o Updated interactive molecular dynamics (IMD) features for the current
      implementation
    o Documentation for new anaglyph stereo feature
    o Documented new RMSD fit startup feature

Known bugs
----------
  Please visit the VMD web site for information on known bugs,
  workarounds, and fixes:
      http://www.ks.uiuc.edu/Research/vmd/

Cost and Availability
---------------------
  BioCoRE, JMV, MDTools, NAMD, VMD and the Structural Biology Software
Database represent the broad efforts of the Theoretical Biophysics Group,
an NIH Resource for Macromolecular Modeling and Bioinformatics, designed
to develop and distribute free, effective tools (with source code) for
molecular dynamics studies in structural biology.
For more information, see:
  http://www.ks.uiuc.edu/Research/biocore/
  http://www.ks.uiuc.edu/Research/NAMD/
  http://www.ks.uiuc.edu/Research/VMD/
  http://www.ks.uiuc.edu/Development/biosoftdb/
  http://www.ks.uiuc.edu/Development/JMV/
  http://www.ks.uiuc.edu/Development/MDTools/

The VMD project is funded by the National Institutes of Health
(grant number PHS 5 P41 RR05969).

Disclaimer and Copyright
------------------------
  VMD is Copyright (c) 1995-2001 the Board of Trustees of the
University of Illinois and others.

The terms for using, copying, modifying, and distributing VMD are
specified in the file LICENSE. If you use VMD in a way you think is
interesting or novel, we would like to know about it.

The authors request that any published work which utilizes VMD
includes a reference to the VMD web page:

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

and/or the following reference:

  Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular
  Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.

Documentation
-------------
  Three VMD manuals are available which describe how to install,
use, and modify VMD. The VMD installation guide, is contained in
the VMD distribution in the file "doc/ig.ps".
The User's Guide and Programmer's Guide are available separately
(due to size) from the VMD web site. Quick help may be accessed
by pressing the "Help" button on the main VMD form, or by typing
help in the VMD command window. This will bring up the VMD
quick help page, and will lead you to several other VMD help files
and manuals.

Quick Installation Instructions
-------------------------------
The Windows version of VMD is distributed as a self-extracting
archive, and should be entirely self explanatory. Detailed instructions
for compiling this version of VMD can be found in the installation guide.
For quick installation of the binary distribution for Unix do the following:

  1) uncompress and untar the distribution into a working directory.
     In this working directory, there are several subdirectories such
     as bin, src, doc, data, as well as this README and a configure script.
     Change to this working directory after the unpacking is complete.

  2) Edit the file 'configure'; change the values for
     the $install_library_dir and $install_bin_dir to a directory in
     which vmd data files and executables should be installed:

     $install_bin_dir is the location of the startup script 'vmd'.
     It should be located in the path of users interested in running VMD.

     $install_library_dir is the location of all other VMD files.
     This included the binary and helper scripts. It should not be
     in the path.

  3) A Makefile must be generated based on these configuration variables
     by running "./configure".

  4) After configuration is complete, cd to the src directory,
     and type "make install". This will install VMD in the two
     directories listed above. Note that running "make install"
     twice will print error messages because you are attempting to
     overwrite some read-only files. This should be fine.

  5) When installed, type 'vmd' to start (make sure the
     $install_bin_dir directory is in your path).

Required Libraries
------------------
  VMD requires several libraries and programs for various of its functions.
In particular, it uses GL or OpenGL based 3-D rendering, and will require
that you have the appropriate GL or OpenGL libraries on your system.
Other programs are required by some of VMD's optional features.
Please visit the VMD web site for more information:
  http://www.ks.uiuc.edu/Research/vmd/

For problems, questions, or suggestions, send e-mail to 'vmd_at_ks.uiuc.edu'.

  VMD Development Team
  Theoretical Biophysics Group
  University of Illinois and Beckman Institute
  405 N. Matthews
  Urbana, IL 61801
  TBG: http://www.ks.uiuc.edu/
  VMD: http://www.ks.uiuc.edu/Research/vmd/

README for VMD; last modified April 22, 2001 by John Stone 

-- 
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