VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 05 2003 - 14:53:13 CST

Dear VMD-L,
  I've just posted VMD 1.8.2 on the web site for download:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.2/

For those of you that haven't seen the beta versions we have had,
here's the list of new features and improvements found in this version:

What's new in VMD 1.8.2?
------------------------
  User Documentation Updates
    o New plugin documentation details the features of existing plugins,
      and covers development and compilation of new pugins.
    o Source code documentation is provided online and is updated nightly.

  User Interface Changes
    o The molecule browser now lists the number of volumetric data sets
      loaded into a molecule under a new "Vol" column.
    o The molecule browser pop-up menu has some new items taken from the
      File menu, and eliminates some unnecessary items from the molecule menu.

  New Features
    o A single representation can now be made to draw multiple trajectory
      frames or coordinate sets simultaneously, with a simple text-based
      frame selection control found in the "Trajectory" tab in the
      graphical representations window.
    o A new "color by Timestep" method has been implemented which
      complements the new "draw multiple frames" feature. Using this feature
      it is easier to visualize what structural arrangements occur at a
      given point in a simulation.
    o The Isosurface representation now produces smoothed surface normals
      rather than flat-shaded triangles, and renders them using efficient
      triangle mesh primitives.
    o New 'autoionize' plugin for adding ions to solvated systems
    o New 'rmsd' plugin replacing the old RMSD script shipped with previous
      versions of VMD.
    o New 'pdbtool' plugin providing an easy interface for automatically
      downloading PDB structures, viewing their entry at the PDB web site
      and looking up their entry in the SCOP database.
    o The 'Snapshot' rendering mode in VMD now supports writing images in
      several formats: PPM (.ppm), Targa (.tga), Windows Bitmap (.bmp),
      and SGI RGB (.rgb). The desired image file format is automatically
      recognized by the file extension. Unrecognized image format extensions
      default to the old behavior.

  New and improved file import and export
    o New Amber "binpos" coordinate file reader plugin
    o New Autodock grid map file reader plugin
    o New Charmm coordinate file reader plugin
    o New CPMD file reader plugin
    o New Delphi "phi" potential map reader plugin
    o New Delphi/GRASP "grd" potential map reader plugin
    o New Molden file reader plugin (currently reads atom coordinates only)
    o New Xtalview "fsfour" electron density map reader plugin
    o Amber CRD trajectory file reader now supports periodic cell information,
      and contains better CRD writing code.
    o The Charmm DCD reader plugin now reads periodic cell information,
      and supports large (greater than 2GB) files on 32-bit Unix platforms.
    o Significantly improved Gaussian "cube" file reader plugin
    o Gromacs file readers now support periodic cell information as well as
      large (greater than 2GB) files on 32-bit Unix platforms.
    o Updated XYZ reader plugin now supports more formats, including XYZ
      trajectories.

  General Improvements and Bug Fixes
    o AutoIMD plugin includes many improvements and bug fixes, and is now
      more usable with local machines as well as clusters and queuing systems.
    o Sequence viewer plugin now supports viewing nucleic acid sequences,
      and now marks its highlighted representation with a special name.
    o VMD's internal Tcl use has been updated to match Tcl 8.4.x
      recommended techniques.
    o The VMD 'logfile' command is now implemented by a Tcl script rather
      than being hard-coded.
    Fixed PRs: 297, 314, 318, 319, 320, 321, 341

Known bugs
----------
  Visit the VMD page 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 and Computational
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/Research/jmv/
  http://www.ks.uiuc.edu/Development/biosoftdb/
  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) 1995-2003 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.

The native MacOS X version of VMD is packaged as a disk image and is
extracted by opening the disk image, and dragging the "VMD" application
contained inside into an appropriate directory.

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, be sure
     that you installing into a clean target directory and not overwriting
     an existing version of VMD (which would otherwise give problems):

     $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. Similarly, if you have incorrectly
     specified the target installation directories or attempt to overwrite
     an existing VMD installation, you will get error messages.

  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 and Computational 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 3, 2003 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