From: John Stone (
Date: Thu Nov 07 2002 - 15:11:38 CST

Dear VMD-L,
  I thought this might be of interest to people looking for stereo flat
panel displays. I recently added new code supporting these DTI displays
in VMD 1.8 alpha 29.


----- Forwarded message from Mike Doolin <> -----

From: "Mike Doolin" <>
To: "John Stone" <>
Subject: Re: VMD 1.8 alpha 29 available for testing!
Date: Thu, 7 Nov 2002 11:06:21 -0500

Hi John - thanks for the update on VMD. As you know, we have tested the alpha 29 version extensively here with our switchable 2D/3D flat panel displays - both the 15" and the 18.1" sizes - and all we can say is WOW! The combination of your software and our no-glasses 3D Display is just great! We've seen lots of 3D software over the years for scientific visualization, but the VMD package is truly extraordinary. The images really do jump off the screen and hang in space, and VMD's extensive viewing choices and manipulation options combined with the extra depth dimension delivers huge amounts of information that is simply not available in a flat image.
We will be doing an email release soon to let our customers know of your support for our 2D/3D Displays.

If your VMD users would like to see these remarkable displays in action, both sizes will be in selected CompUSA stores in ten cities soon, probably toward the end of next week or by Monday the 18th. We will be doing an email news release shortly to that effect, and we will identify the cities in that announcement. The displays will also be available for purchase on CompUSA's web site, and we'll be including that site address in one of the emails. You may want to pass this info along to selected VMD users. Sales of these displays have always been brisk, and for that reason it has been difficult for us to have enough demonstration units available so that everyone who wanted to see the technology before purchase was able to. Many customers bought without ever seeing a display, and while we certainly can't complain about that, we know that there are many folks who would like to see the display before purchase. The availability through CompUSA should help alleviate that and expose these displays to many more peop

If you want to send anyone directly to our site for more info, here's the link:

Thanks again for your support. We appreciate it.

Mike Doolin
Marketing Manager
Dimension Technologies Inc.
  ----- Original Message -----
  From: John Stone
  To: ;
  Sent: Wednesday, November 06, 2002 3:40 PM
  Subject: Re: VMD 1.8 alpha 29 available for testing!

  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

----- End forwarded message -----

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