From: John Stone (
Date: Wed Nov 06 2002 - 14:40:16 CST

Dear VMD-L,
  I belatedly realized that I missed mentioning several of the more
interesting recently added features in the new alpha 29 test version:

    o A new ribbons representation called "NewRibbons".
      This is not quite finished yet, but you can see where it is heading.

    o New "throb" coloring scheme that cycles colors based on wall clock time

    o New "DTI SideBySide" stereo mode for DTI flat panel stereoscopic displays.

    o Automatic recognition of WireGL-based display systems

    o Support for the FreeVR virtual reality system.
      (only enabled in the Solaris binaries so far...)

  John Stone

On Fri, Nov 01, 2002 at 05:52:09PM -0600, John Stone wrote:
> Dear VMD-L,
> I've just made a new distribution of VMD 1.8 alpha 29 available
> for testing on our web site:
> 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:
> If you encounter new bugs or problems with this test version of VMD,
> please let us know. (condensed feature list below)
> Thanks,
> John Stone
> 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: Phone: 217-244-3349
> WWW: Fax: 217-244-6078

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:                 Phone: 217-244-3349              
  WWW:      Fax: 217-244-6078