VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 07 2000 - 17:59:02 CST

Dear VMD-L,
  I'm happy to announce that we have just made the production version
of VMD 1.4 available for download at the VMD web site:
  http://www.ks.uiuc.edu/Research/vmd/

Along with the release of VMD 1.4, we have changed to a new software
registration that should be much nicer than the old system. The new
system will ask you to supply a password which (if you remember it) will
allow you to download all future VMD and NAMD versions without having
to re-register again. The new registration page will also allow you to
have your browser save a cookie (if you select the cookie box) so that you
don't have to type in your password, but rather have your web browser
remember your cookie for you. Since this download and registration
system is new, I'm announcing the availability of VMD 1.4 to the VMD-L
list first, since most of you are already experienced VMD users. Please
let us know if you have any trouble downloading using this new system.

As with any software release, there were features and improvements that
we had been hoping to squeeze into VMD 1.4, but we felt that it was time
to make the software available, and to put these features into an update
release later this winter/spring. The timing and contents of the next
release will depend a lot on the feedback we get from the user community,
especially users of thw new Windows version of VMD.
As always, we appreciate your comments and opinions.

Now, without further delay, here is the README from the new VMD 1.4:

                       README file for VMD 1.4
---------------------------------------------------------------------------

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 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, 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 1.4?
----------------------
  Platform Support
    o Full support for Microsoft Windows 95/98/NT with hardware
      accelerated OpenGL based 3-D rendering.

  New Features
    o Support for reading Gromos96 trajectories (ASCII-only).
    o Completely rewritten 3-D Tracker support which supports
      haptic force feedback, improved tools, and new user interface
      elements.
    o Completely redesigned interactive molecular dynamics support code,
      which replaces the older MDComm code. The new code works on all
      supported Unix platforms, and is built into VMD by default since
      it is very small and efficient.
    o Completely new font rendering code, which is more flexible, and
      supports new sizing capabilities.
    o New DCD file reader automatically performs byte-swapping when
      reading little-endian files on a big-endian machine, and vice versa.
    o Completely rewritten regular expression handling system. VMD now
      uses PERL style regular expressions, and is much more efficient.
    o The OpenGL versions of VMD now implement a fast "screen-door"
      transparency algorithm which provides a basic transparency feature
      with no degradation to overall VMD rendering performance.
      Publication quality rendering of transparency effects still requires
      the use of external ray tracing software.
    o New backface culling feature helps improve rendering performance
      on low-end machines with minimalistic graphics hardware.
 
  General Improvements and Bug Fixes
    o Greatly reduced CPU time consumption when idle (not rotating etc..)
      VMD keeps track of the exact circumstances that require a display
      redraw, and only runs the graphics hardware when necessary, rather
      than continously as previous versions did.
    o Improvements in several internal data structures, resulting
      in increases in molecule loading speed for large files. Tests
      with a 206,750 atom system yielded a 20-fold increase in speed over
      previous versions of VMD.
    o The "within" distance-based atom selections now run 50 to 100 times
      faster through the use of a grid-based spatial decomposition.
    o The "same residue as" atom selections now run 50 to 100 times
      faster through the use of a hash-table-based binned acceleration
      data structure..
    o Improved the depth cueing code in VMD, so that it works much better
      on all platforms. The depth cueing effect is much more pronounced,
      and is no longer affected by bugs in old graphics accelerator
      implementations.
    o The Radiance, Raster3D, and Tachyon scene exports have been improved
      substantially over previous versions of VMD, and now support current
      versions of these packages.
    o The PostScript renderer feature now runs much faster, generates smaller
      files, and supports more primitives than previous versions. Several
      bugs in memory deallocation have also been fixed.
    o Updated the VMD code that implements "mol pdbload" for direct loading
      of proteins from the RCSB, using their new database layout.
    o Fixes to OpenGL Display Device code for window position and size.
    o Improved overall efficiency of many parts of VMD, and cleaned up
      several of its basic classes/templates.
    o Extensive audit of VMD 1.4 documentation, including rewritten
      chapters for interactive molecular dynamics simulations, and
      VMD 3-D tracker support.
    o Mesa versions of VMD are now built using Mesa 3.1
    o VMD no longer depends on the GNU libg++ string classes, it uses
      its own string class, which is much smaller and more efficient for
      the tasks VMD uses it for. This also simplifies the VMD compilation
      process substantially.

  User Interface Changes
    o Several of the "popup" menu interfaces in VMD have been eliminated
      in favor of the portable "Form" based interfaces.
    o New "tool selection" button in the graphics form.
    o New "culling" button in the display form.
    o Completely redesigned Tracker form.
    o Redesigned Sim form.

  User Documentation Updates
    o New Windows platform notes in the VMD installation guide
    o Updated sections in the User guide pertaining to interactive
      molecular dynamics with NAMD, and the use of spatial trackers
      and haptic feedback devices with VMD.

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 range 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/collaboratory/

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.

Portions of VMD code are Copyright (c) 1997-1998 Andrew Dalke

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.

Please take a few minutes to fill out a registration form at
http://www.ks.uiuc.edu/Research/vmd/VMDregistration.html
if you are going to use VMD.

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 postscript documentation files are available for VMD which
describe how to install, use, and modify VMD. One, the installation
guide, is contained in the VMD distribution in the file doc/ig.ps .
The other two, the User's Guide and Programmer's Guide are available
separately (due to size) from the VMD web site.

  A quick help file in HTML format, 'vmd_help.html' is also available,
in the 'data' directory of the distribution. This file may be viewed
by any HTML viewer, and is used to provide on-line help for VMD when
it is running.

For the latest information on VMD, please see the VMD WWW home page:
  http://www.ks.uiuc.edu/Research/vmd/

This page contains links to HTML versions of all three VMD manuals
listed above, and info on the latest release of the program. A
brief VMD FAQ is also available, and can be found either by looking
at the VMD home page, or directly via the URL:
  http://www.ks.uiuc.edu/Research/vmd/vmd_faq.html

Installation
------------
  Detailed instructions for compiling this version of VMD can be found
in the installation guide, ig.ps. 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 WWW: http://www.ks.uiuc.edu/
  VMD WWW: http://www.ks.uiuc.edu/Research/vmd/

README for VMD; last modified January 7, 2000 by John Stone 

-- 
Theoretical Biophysics Group   Email: johns_at_ks.uiuc.edu
Beckman Institute              http://www.ks.uiuc.edu/~johns/
University of Illinois         Phone:  (217) 244-3349
405 N. Mathews  Ave              FAX:  (217) 244-6078 
Urbana, IL 61801, USA          Unix Is Good For You!!!