VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 22 2000 - 17:17:04 CST

         VMD "Visual Molecular Dynamics" 1.6 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. 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, 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
                                                December 22, 2000

                       README file for VMD 1.6
---------------------------------------------------------------------------

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.

  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, Radiance, Raster3D, Rayshade,
    and Tachyon.

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

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

What's new in VMD 1.6?
----------------------
  New Features
    o New "mol load webpdb XXXX" internet based PDB loading on both
      Windows and Unix platforms.
    o Python scripting interface available on Linux, Solaris, and IRIX versions
    o Wireframe rendering modes for MSMS and Surf (new control counter on
      the MSMS/Surf rep subforms)
    o Support for generation of RenderMan .RIB files from VMD scenes.
    o New platform support for Linux on Alpha processors
    o New platform support for Linux on PowerPC processors
    o Improvements supporting "VMD chat", a Tcl based collaborative VMD
      session feature to allow two or more people to connect their VMD
      sessions over a network. The "VMD chat" script is provided in
      the VMD script library.
    o Improvements supporting "ZoomSeq" sequence-based highlighting,
      selection, and coloring, as well as rudimentary internet based sequence
      search/query through new Tcl scripts, also to be found in the VMD
      script library soon after VMD 1.6 is released.
 
  General Improvements and Bug Fixes
    o Windows version of VMD now implements mouse capture so that you can
      drag the mouse outside of the graphics window while doing rotations,
      translations, scaling, and other mouse dragging operations.
    o Improved interactive rendering speed of molecular surfaces by a factor
      of two or more on most platforms.
    o Improved OpenGL materials rendering and gave VMD better looking
      default material properties.
    o Tachyon ray tracer binaries are now packaged along with VMD on all
      supported platforms. Now includes faster version of Tachyon.
    o Added the ability for Tcl code to capture VMD events as through
      the logfile mechanism, but through a Tcl variable, so that one VMD
      can easily remote control other VMD's through a bit of Tcl sockets code.
    o Significant speed increases for many common VMD commands,
      many commands are 5 to 200 times faster now, using new Tcl 8.x
      interpreter interface.
    o Made it easier to customize size/position of the VMD command window
      on Unix versions of VMD.
    o Improved VMD startup script, now works beter on HP-UX systems
    o No longer built with TclX/TkX, these are now removed from distribution.
    o Trimmed out excess baggage in VMD scripts directory
    o Built with FLTK 1.0.9
    o Built with VRPN 5.01
    o Fixed PRs: 60, 101, 106, 108, 109, 110, 111, 112, 113, 114, 124

  User Interface Changes
    o New Tcl/Tk based RMSD fit GUI
    o Save state uses a GUI dialog now when possible.
    o The representation browser in the graphics form no longer lists the
      numbers associated with a draw style, to conserve space and improve
      readability.

  User Documentation Updates
    o Doucmentation for new Python scripting interfaces.
    o Updated various sections in User's guide, particularly relating to new
      rendering features, RMSD fit, etc.
    o Started lengthy update to Programmer's guide.
    o Added commit email capability to CVS, may make it an option
      for read-only CVS users as well.
    o significant improvements to Tcl scripting section

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
---------------------
  VMD, NAMD, and BioCoRE 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/VMD/
  http://www.ks.uiuc.edu/Research/NAMD/
  http://www.ks.uiuc.edu/Research/biocore/

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

Disclaimer and Copyright
------------------------
  VMD is Copyright (c) 1995-2000 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/

  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 December 22, 2000 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