VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 14 2000 - 02:38:08 CDT

Dear VMD-L,
  We have just made VMD 1.6a1 available for download on the
VMD downloads page:
  http://www.ks.uiuc.edu/Development/Download/download.cgi
 
Some short commentary on what we've been up to for VMD 1.6a1:
  Since we made a lot of changes in 1.6a1, we created a few bugs
here and there, and 1.6a2 fixes some of those bugs, as well as
fixing some longer standing bugs (PRs 106, 111, 112) in handling
command-line parameters on Unix, reading Amber PARM/CRD files that have extra
are missing line feeds, and potential crashes when reading corrupt or
otherwise improperly formatted PARM/CRD files. We have also fixed
a few small display update and GUI bugs since 1.6a1.

VMD now handles abnormal termination conditions slightly more gracefully
than in the past. It will pause before exiting/aborting so that the user
has time to read any output left in VMD's command window. This also lets
the "vmd -h" command line option work much more effectively on Unix systems.
In addition, we have fixed a problem with the new Surf and MSMS interface
code that could cause bad things to happen in VMD 1.6a1 when using them with
animations etc.

Lastly, we have upgraded the functionality of
the Renderman output using more of its capabilities. People interested
in using the Renderman output can check out BMRT ("Blue Moon Rendering Tools")
at http://www.bmrt.org/ BMRT is a free Renderman compliant renderer
written by Larry Gritz. Those of you with commercial rendering software
such as Maya or Pixar's own Renderman can also take advantage of this new
feature of VMD.

Upcoming Changes in VMD:
  We're in the process of rewriting the PostScript renderer in VMD so that
it will run faster, produce better output in general, and a new feature
we're looking into is to support PostScript Level 3, which has support for
Gouraud shaded triangles, quads, etc, which VMD could use to produce MUCH
better looking vector PostScript output.

Something I have been thinking about, now that we are shipping pre-compiled
binaries of Tachyon (my multiprocessor ray tracer) with VMD, would be a new
interface to Tachyon which avoids writing huge scene files to disk, so that
people can render complex VMD scenes much more quickly than they can now.
(One of our local scientists just rendered an image last weekend that
 generated a 118 megabyte scene file. VMD and Tachyon spent something like
 6 or 8 minutes doing file I/O, and less than 60 seconds to actually
 render the scene, so clearly there are speed gains to be made by avoiding
 writing to files altogether, except for the case when the user _wants_
 the scene written to a file for some reason.)

We have some new features in the works for VMD 1.6 still, but I'll
mention those in more detail in a future email.

Other interesting VMD news items of late:
  Did you know that you can run a Tcl-based web server from within VMD?
  We have taken a Tcl web server and run it from within a VMD session
  successfully. It works pretty well. The initial messing around we did
  was just to see if it would work, but this brings up the interesting
  question of: Is there anything that scientists could use such a capability
  for? Would it be useful for people to point their netscape at their VMD
  as another means of interacting with it?? Tell us what you think!
  It should be possible to modify a Tcl web browser to run Tcl procedures
  which query/set VMD variables and change the state of the program. We
  haven't actually gone that far yet, but it would be an interesting thing
  to experiment with. If any of you are interested in this, send us a
  note, and we can tell you what we've done already and how you can do it
  for yourself in a little more detail.

As always, please let us know if you have questions about anything
or have bug reports etc.

Thanks for using VMD!!!
 
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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