VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 05 2001 - 21:14:37 CST

Dear VMD-L,
  I have just built a test version, VMD 1.7.1b1, that I'd
like to get user feedback on. This new version includes
several new features that required changes to our graphics code,
so that's one of the major items I'd like feedback on. If people
have any trouble running this version on their graphics boards, please
let us know. This is the first version of VMD to use the
texture mapping hardware on the graphics accelerators, specifically
it now makes use of 3-D texturing in support of new volumetric data
display for potential maps, isosurfaces, EDM files, etc. Those
people wishing to try out these new features with some of the
early scripts we've got for reading volumetric data files should
feel free to email us.

You can download VMD 1.7.1b1 from:
  http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

The full list of features and improvements in this test version
is included below.

Thanks,
  John Stone
  johns_at_ks.uiuc.edu

What's new in VMD 1.7.1?
------------------------
  New Features
    o New volume rendering features including isosurface display,
      volume slicing with support for hardware accelerated 3-D
      texture mapping, and a Tcl volume data loader interface.
    o Support for scanline-interleaved stereoscopic rendering for
      hardware such as the Eye3D stereo glasses and decoders.

  General Improvements and Bug Fixes
    o Multi-level OpenGL stipple-based "screen door" transparency. Now
      implements varying levels of transparency.
    o Improved support for WireGL cluster-based rendering and tiled display
      walls.
    o The IMD code now closes down active socket connections more
      carefully, allowing the kernel to complete any in-progress
      write operations before closing the socket.
    o Tachyon scene export improved with new camera parameters for
      matched perspective views with VMD.
    o POV-Ray scene export improved with new camera parameters and
      support for orthographic views, shadow control, and matched
      perspective camera views.
    o Replaced DNA example molecule with a better one.
    o H-bond shown in the H-bond rep are now pickable.
    o Added code to read the unit cell data from Charmm trajectory files.
    o Improved robustness and error handling when reading Raster3D
      scene files. Fixed Raster3D file reading crash.
    o Eliminated atom selection and Tcl related memory leaks
    Fixed PRs: 168, 170, 171, 172

  User Interface Changes
    o Users can select either FLTK or Tk file browsers according to
      their personal preference. Some people prefer the Windows-like
      function of the Tk browsers, while others like the filename
      completion of the FLTK file browser. This is configured by setting
      the VMDFILECHOOSER environment variable.
    o Reverted behavior of the edit form old "-1" index use.

  User Documentation Updates
    o Updated the betacolor example script included in the docs for
      new versions of VMD.
    o Updated the animation scripts in the script library for new
      versions of VMD.
    o Improved index entries pertaining to lighting and shading.

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 December 5, 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