VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 17 1999 - 02:08:02 CST

     VMD "Visual Molecular Dynamics" 1.3 Beta 1 Announcement
     --------------------------------------------------------
  The Theoretical Biophysics group at the University of Illinois and the
Beckman Institute For Advanced Science and Technology is happy to
announce the availability of Beta 1 of VMD 1.3. VMD is a package
for the visualization 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 HP, Linux, Sun, and SGI
Unix systems. The 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.

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

Changes to VMD 1.3b1 since VMD 1.3a2:
-------------------------------------
   Upgraded VMD version of Mesa to 3.0 from 2.6
   Upgraded VMD version of Tcl/Tk/TclX to 8.0.4 from 8.0p2
   Several changes to configure script /wrt IRIX6 builds.
   Rebuilt local IRIX6 tcl/tk/tclx libs with "-G 0" to avoid gp_overflow
     errors at link time.
   Rebuilt surf_IRIX6, and stride_IRIX6 for -mips3
   IRIX6 configuration now uses -mips3 instead of -mips4
   Rebuilt local libraries for IRIX6 binary distribution, old
     ones forced the resulting executable to be mips4-only...
   Bug reported in XYZ file reading (existed in previous revs too..)
   Bug reported in CRD file reading (existed in previous revs too..)
   Analysis of 1999 VMD User Survey Results / re-send to unresponsive users
   LICENSE file missing from Linux RPM distribution, fixing.
   Identified a bug in VMD's scripting language and/or docs. The
     coloring routines can't do "by resid". This is either a bug, or an
     incomplete implementation. Still under investigation.
   May have identified a long standing rendering bug in VMD, likely
     incorrect display of specular highlights (phong equation) due to a
     bad transformation stack. Looks incorrect in current OpenGL version.
     Still under investigation. (would affect all OpenGL versions for sure..)
   Identified a bug in the OpenGL version tracker display/transform code.
   Identified a bug in the OpenGL version Cave input devices (kbd, trackers)
   Identified 64-bit portability bugs in VMD's rendering code.
   Updated many documentation items to be correct for VMD 1.3.
   Added information on new target platforms in web documentation.
   Fixed IRIX6 binary distribution, was missing stride and surf binaries.
   Fixed permissions of OSF1 stride and surf binaries for distributions.
   VMD successfully communicates with VRPN based trackers.
   Additional work on fixing VMD for compilation with xlC on AIX 4.2.

Changes to VMD 1.3a2 since VMD 1.3a1:
-------------------------------------
   Fixed a few small bugs in the configure script, with respect to
     the ACC, GCC, KCC, and EGCS build options, and with the
   HPUX10 build configurations.
   CAVE option is now part of all IRIX builds (both GL and OpenGL) by default.
   Eliminated double linkage of xforms libraries, and a UIUC local item
     in the configure script.
   Improved all IRIX builds, eliminated unnecessary libraries from
     linking, especially the old libmalloc.
   Improved Tracker List, so that user can differentiate between
     VRPN trackers, and the old UNC trackers.
   IRIX6 builds of VMD using OpenGL and the Cave.
   Fixed configure script for OpenGL builds of VMD for the Cave.
   Updated all VMD Tracker classes, fixed name collisions with VRPN library
   First rev of VRPN based VR tracker/button/force support code for VMD.
   Updates to Cave tracker code for keeping up with VRPN related changes.
   Updates to Cave rendering code, first rev to compile under both GL and OpenGL
   Numerous fixes for compiling with xlC on AIX 4.2, still more left to go.
   Small IRIX6 code fixes.

Changes to VMD 1.3a1 since VMD 1.2:
-----------------------------------
   Ported VMD to Solaris 7 x86.
   Several fixes to VMD for builds on DEC Alpha and other LP64 platforms,
     still needs work though.
   First version of VMD that works with FLTK for GUI instead of XForms.
   Significant amounts of changes for future versions of VMD on Win32
   First version of text-only VMD that runs on Win32.
   Added new support for Tachyon Parallel / Multiprocessor Ray Tracer.
   First round of Win32 changes integrated into main source treee.
   Added new matrix code to replace some external tcl code and LASSP tools
   Eliminated the use of LASSP Tools in VMD
   Redesigned the render-snapshot feature to work in a platform independent
     manner. Wrote first implementation on OpenGL builds. Works on Sun, SGI,
     HP, etc. Writes PPM files presently.
   Added new capability to VMD so that user may specify a preferred image
     viewer program.
   Snapshot code now uses user specified image viewer if the environment
     variable is set
   Eliminated some dead code in VMD.

Availability
------------
The software is available for downloading from
http://www.ks.uiuc.edu/Research/vmd/

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)

                                                John Stone
                                                vmd_at_ks.uiuc.edu
                                                February 17th, 1999