VMD-L Mailing List

From: #WONG CHEE HOW# (P7443050C_at_ntu.edu.sg)
Date: Fri Nov 01 2002 - 22:48:10 CST

Hi,

I missed out something. I am downloading the Windows version of 1.8a29

CH Wong

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Saturday, November 02, 2002 7:52 AM
To: vmd-l_at_ks.uiuc.edu; vmd_at_ks.uiuc.edu
Subject: VMD 1.8 alpha 29 available for testing!

Dear VMD-L,
  I've just made a new distribution of VMD 1.8 alpha 29 available
for testing on our web site:
  http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

You'll immediately notice that this version has significant GUI changes,
even when compared with the previous alpha 21 test version.
This version also contains many performance enhancements, new features,
and bug fixes from the previous alpha release. I haven't actually had
time to tally up the full list of changes in the condensed list at
the end of this email, but the full laundry list of changes is available
for your perusal here:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/devel.html

If you encounter new bugs or problems with this test version of VMD,
please let us know. (condensed feature list below)

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

A more condensed (but incomplete) listing of significant changes follows below:

What's new in VMD 1.8 alpha 29?
-------------------------------
  User Interface Changes
    o A new "main" form replaces functionality of the old main form and the
      old molecule menu. The new main form uses a more modern and
      conventional style for loading and saving various files and is
      generally easier to use than the old interface, particularly for
      new users. The new main form uses popup menus for control of the
      the loaded molecules similar to the functionality provided by the old
      molecule menu.
    o New graphical representations form replaces the old one, with
      greatly improved controls for some of the new reps.
    o A new "labels" form integrates the features from the old
      menu and integrates the picked atom information display from the
      old mouse form. The new labels form includes a built in graphing
      feature for measuring geometry properties over trajectories.
    o New file loading and saving forms replace the old ones, with full
      support for dynamic file format support by plugins.

  New Features
    o New user-definable atom selection macros allow new atom selection
      keywords to be defined.
    o New plugin interfaces for file loading and more general VMD extensions
    o New "plugin list" command to find out what plugins are registered in
      VMD.
    o VRML 2.0 scene export for external renderers, rapid prototyping machines,
      and web-based visualization of molecular models.
    o New file loader for NAMD restart files.
    o Per-representation clipping planes can now be used to make cut-away
      views of molecular representation geometry. Up to six clipping planes
      can be added to each rep.
    o New dynamically recalculated "bonds" representation, useful for viewing
      ab-initio simulations.
    o New "display resize" command allows script-based display window size
      control.
    o New "measure bondsearch" command provides a much easier mechanism for
      performing bond search operations within scripts.
    o New "LibTachyon" built-in ray tracing feature for very fast
      ray tracings of VMD scenes (totally eliminates disk I/O for scene files).
    o Supports the newest version of Tachyon which implements directional
      lights, orthographics projections, and other VMD-oriented features.
    o Automatic nearest-atom highlighting mode useful for
      interactive MD simulations and other cases where it is helpful to
      have the nearest atom to the tracker or mouse pointer highlight itself.
      This makes interactive selection much easier, particularly when
      the structure is moving as in a trajectory or interactive simulation.
    o User-defined graphics are now added to existing molecules rather than
      a separate graphics molecule. This allows annotations highlighting
      geometry and other data to be attached to a specific molecule.
    o New graphical user interfaces have replaced the old VMD interfaces
      (see descriptions below).

  General Improvements and Bug Fixes
    o The STL scene export option now supports more geometry than just the
      Surf/MSMS representations.
    o BioCoRE publish/sync works with plugin-based file readers.
    o VMD saved states are now restored much more efficiently.
    o The CAVE and FreeVR code have been significantly improved over previous
      versions. A single binary can now be built with both the CAVE
      and FreeVR options enabled.
    o The OpenGL renderer now caches a significant amount of state,
      eliminating a number expensive OpenGL state manipulation operations
      which. VMD 1.8 uses several OpenGL extensions and new rendering
      techniques all yielding better interactive rendering performance.
    o Renderman export code improvements donated by Grischa R. Meyer.
      The orthographic display mode works well now, and the
      perspective mode is now closer to what is shown in the OpenGL window.
    o Labels get deleted when their molecules get deleted.
    o Colors for atom name and atom type are now assigned based on the first
      non-numeric character, rather than simply the first character. This
      makes atoms named 1H3, for example, be colored the same way as othe
      hydrogen atoms (white), rather than green or some other color. PDB
      files from the RCSB often have atom names numbers as the first
      character, but the number carries no information as to how the atom
      should be colored.
    o Made the Tcl commands "mol load", "mol pdbload", and "mol urlload" return
      the molid of the newly created molecule, or else return an error.
      Previous behavior was to return nothing and ignore all errors.
    o Added a waitfor option to the Tcl animate read/write commands to make
      them load the specified number of frames (or "all") before returning.
      Also made these commands return the number of frames loaded or saved.
    o General improvements to the VMD Python documentation and implemention.
    o Fixed missing state change code for representations that sometimes draw
      as lines, and were incorrectly inheriting their line drawing state from
      preceding representations.
    o Recalculating secondary structure now correctly forces recalculation of
      colors if the rep is colored by structure.
    Fixed PRs: 12, 20, 74, 77, 138, 144, 147, 149, 179, 180, 182, 183, 184,
               190, 197, 198, 201, 202, 208, 209, 210, 211, 212, 213,
               214, 215, 218, 233, 234

  User Documentation Updates
    o Added documentation of several molinfo get/set keywords.
    o Updated sequence viewer documentation
    o The source code documentation is now automated through the use of
      Doxygen, and efforts have recently been made to update the header files
      of important classes with useful comments wherever applicable. 

-- 
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