Subject: Announce: VMD 1.7 Released

From: John Stone <[email-masked]>
Date: Fri, 3 Aug 2001 15:10:40 -0500

Dear CCL,
  VMD 1.7 is now available!

Quick links:
    http://www.ks.uiuc.edu/Research/vmd/           (home page)
    http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/   (VMD 1.7 page)

Full announcement, followed by feature list:

         VMD "Visual Molecular Dynamics" 1.7 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 1.7.  VMD is a package 
for the visualization and analysis of biomolecular systems.  
VMD includes features for animation of molecular dynamics trajectories, 
interactive simulation, sequence browsing and structure highlighting, 
and powerful scripting capabilities. This software is distributed 
free of charge and includes source code, documentation, and precompiled 
binaries for Compaq, IBM, HP, Linux, MacOS-X, 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/

Links to magazine and journal articles about VMD are provided here:
  http://www.ks.uiuc.edu/Research/vmd/allversions/publications.html

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.

What's new in VMD 1.7?
----------------------
  New Features
    o Integrated sequence browsing capabilities are now part of VMD, based
      on the previously available "ZoomSeq" Tcl script, with many
      improvements.  The sequence browser is significantly faster than the
      older separately distributed ZoomSeq script, and will eventually
      provide several new interfaces not included in the production version.
    o Integrated Ramachandran plotting capabilities are now part of VMD.
    o Support for joysticks and other game controller input devices on
      the Windows platforms.
    o Windows versions of VMD now include support for VRPN, haptic feedback
      and interactive molecular dynamics.
    o Unix and Windows versions of VMD now include built-in support for
      Spaceball 6DOF 3-D controllers, which can be used for rotation,
      translation, and scaling.  The Spaceball can be used simultaneously
      with the Mouse, so that one can use the mouse for picking, measuring,
      controlling of user interface menus, while using the Spaceball to
      orient the molecules in 3D.  Future versions of VMD will make the
      Spaceball interface even more powerful.
    o New support for OpenGL ARB multisample antialiasing extension, provides
      multisample antialiasing on Linux/GeForce, Solaris/Expert3D and
      other platforms.
    o An easier-to-use -webhelper flag for use with Unix versions of VMD when
      setting up VMD as a web helper application for PDB files and VMD
      scripts.

  General Improvements and Bug Fixes
    o POV-Ray render export now provides basic support for orthographic
      views, with other renderers to follow.
    o Replaced O(N^2) hydrogen-bond finding code with a call to the bond
      search subroutine, resulting in a 2-4x speedup and better scaling.
    o Postscript scene exports now includes text labels
    o The axes are drawn using lines for Mesa builds of VMD.  Mesa builds
      use software rasterization, so axis lines improve display redraws
      noticably.
    o Atom selection keywords lookups which operate on integer values
      now use a hash table to accelerate keyword list processing for a
      significant speed increase when working with large molecules.
    o Contains improvements donated by Sergei Izrailev, which make VMD more
      suitable for use as a library callable from within other applications.
    o Updated Tcl and Python callbacks to pass shift key state so that
      scripts like ZoomSeq can do more complex selection and highlighting.
    o The 'mol pdbload' and 'mol load webpdb' functions now download
      compressed PDB files from the RCSB, which is both faster and generally
      more reliable than downloading uncompressed files from the RCSB server.
    o New "phi" and "psi" angle atom selection keywords, which can be used
      to query and modify phi and psi angles.
    o Python commands can now be run with 'gopython -command "foo"'
    o Added "light pos" commands for setting the position of lights
      and restoring them to their default values
    o New "material delete" command
    o VMD is now built with Tcl 8.3.3 and Tk 8.3.3, which have improved
      support for secure http and many other omponents.
    o VMD is now built with Python 2.0.1
    o VMD is now built with VRPN 6.0
    o Rewritten MSMS interface, fixes PR 20
    o Fixed PRs: 20, 157, 158, 159, 160, 161, 162, 163, 164, 165

  User Interface Changes
    o All VMD file browsers are now implemented in Tk by default rather than
      FLTK, as Tk provides a much better match with the Win32 filesystem
      conventions.  The FLTK file browser did not have a good Win32 interface
      (no drive letters) so it is now only used as a fall-back when Tk is
      not compiled into VMD.
    o The counters for selecting frames in the Edit form now range
      from 0 to the number of frames for the molecule, looping back to 0
      or numframes-1 when the counters hit the end of the valid range.
      The "Skip" counter was renamed to "Step" and its range was limited
      to "1" or higher.
    o New sequence browsing window, and associated menus
    o Eliminated support for the old XForms GUI toolkit.
    o IRIX versions of VMD now use xterms instead of winterms,
      and they use the default font rather than Screen11 which used to
      cause some problems for people displaying remotely to non-SGI
      machines.

  User Documentation Updates
    o Added documentation for the "frame" atom selection keyword.
    o New molecular analysis section explaining how to use VMD for common
      analysis tasks, particularly those involving atom selections and
      molecule data.
    o Added documentation for new sequence browsing features
    o Added documentation for new Ramachandran plotting feature
    o Added documentation for new Spaceball and Joystick input devices
      on Windows and Unix.

We are eager to hear from you, and thank you for using our software!

                                                John Stone
                                                [email-masked]

-- 
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: [email-masked]                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078