VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 25 2000 - 14:18:24 CDT

Dear VMD-L,
  We have just made VMD 1.5b1 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 1.5b1:

Docs: 

----
Justin, Dave, and I have recently put some effort into updating
the VMD docs again, and I've finally gotten latex2html to build
us a passable HTML version of the docs.  The new docs are already
up and available at:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.5/docs.html
If you have any comments or suggestions about the new docs, please
send us a note.  I plan on doing some more work on the docs before
the final VMD 1.5 is released, so your suggestions will help me a lot.
VMD:
---
You'll notice a new "Materials" form in VMD 1.5b1, which replaces
the simple opaque/transparent material button that was in the Graphics
form of previous versions of VMD.  The Graphics form now contains a 
pull-down list of available materials, and it contains two unchangeable
default materials "opaque" and "transparent" which are always there for
the user's convenience.  To create new materials, open the materials form,
and press the create new button, it will copy whichever material is
selected in its listbox, and create a new one with a default name.  
You can then change the material name to whatever you like, and this
new material will then appear in the pull-down list in the graphics
form.  The material properties are used to control the way VMD shades
the surfaces of a given molecular representation.  You can use them 
to make your atoms shinier, duller, bright, dim, transparent, etc.   
The material properties are particularly useful when you want to make
grayscale images of your molecule for articles, or when rendering 
using external ray tracing programs where you want the molecule shading
to look "just so".  We are eager to hear your comments about this
new feature, and any suggestions you might have for it before the
release of the final version of VMD 1.5, which will happen in a few
weeks.
There is a new "cancel" button in the Molecule form, which can
be used to stop VMD in the middle of loading very lengthy trajectory
files.  This can be useful if you make a mistake and load that huge
3GB trajectory file that you accidentally clicked on, or if you just
change your mind halfway through loading something.  Give it a spin!
During the next few weeks I (John) will be unavailable via email, so
you should make sure send any VMD related correspondence to 
vmd_at_ks.uiuc.edu to insure a timely reply.  I will answer any other emails
when I return on June 17.  I strongly encourage people to try out 
VMD 1.5b1 and send us comments, we really want this to be a great 
version of VMD!!
Snippet from the new 1.5b1 README:
What's new in VMD 1.5b1? (major changes since 1.4)
------------------------
  New Features
    o Support for several Gromacs structure and trajectory file formats:
      *** Note: 1.5a2 had a bug which is now fixed in 1.5b1
      - Can read .gro for structure (concatenated multiple-frame .gro
        files are read automatically) (variable precision ASCII format)
      - Can read .g96 for structure (concatenated multiple-frame .g96
        files are read automatically) (fixed high precision ASCII format)
      - Can read .trr for trajectory (full precision, portable binary format)
      - Can read .xtc for trajectory (variable precision, compressed binary
        format)
      Note: Doesn't support .trj files, or combined run-input files yet, but
            Gromacs users can run trjconv to convert these into one of the
            formats that VMD can read.
    o Windows versions of VMD now write their snapshot images as
      24-bit color Windows Bitmaps (.bmp) files directly.
    o Added the ability to modify the name, type, resname, resid
      chain, and segname of a selection of atoms.
    o Entirely new rendering capabilities implementing "material"
      properties, for user control of ambient, diffuse, and specular
      reflectivity, as well as surface shininess.
  General Improvements and Bug Fixes
    o Improved the rendering output for Raster3D and Tachyon
    o General improvements to all renderer output.
    o Major revision of IMD (Interactive MD) features in VMD.
    o The Unix versions of VMD are now built with FLTK instead of XForms,
      this brings both the Unix and Windows versions of VMD to using exactly
      the same GUI, and decreases VMD's code/binary size noticably.
    o New OpenGL code to allow SGI O2s to support stereoscopic display
      with 16-bit depth buffering and and 12-bit color.
    o Fixed quite a few of the outstanding problem reports (bugs)
      that were sent in on previous versions of VMD.
      PRs fixed: 5, 7, 10, 19, 23, 29, 58, 64, 68, 75, 76, 78,
                 79, 81, 83, 87, 88, 89, 90, 94, 95, 96, 97, 98, 100
    o Rewrote large parts of the VMD display command system.
  User Interface Changes
    o New GUI color scheme, using lighter colors which are easier on most
      people's eyes, particularly with laptops, projectors, etc.
    o New "Mouse" form which supercedes the old "popup menu" found in
      all of the previous Unix versions of VMD.  The Mouse menu is
      identical on both Windows and Unix, unlike the previous versions of
      VMD where the Windows version had no analog to the popup menu.
    o New "Materials" form which provides controls over rendering
      properties for representations.  (controls for shininess,
      diffuse, ambient and specular reflectivity etc)
    o Renamed the "Mol" and "Sim" forms to their longer names for increased
      intuitiveness to new users.
    o New "Cancel" button on the Molecule form providing the ability to
      cancel loading of very large trajectory files.
  User Documentation Updates
    o Improved HTML version of documentation (new rev of latex2html)
    o Improved PDF version of documentation, now uses better scalable fonts
    o Updated the VMD tutorial to cover new GUI features
    o Updated docs on rendering to snapshots and to external renderers
    o Many updates to sections explaining the VMD GUI, particularly
      the new GUI features.
Thanks for using VMD!!!
  John Stone
  vmd_at_ks.uiuc.edu
-- 
Theoretical Biophysics Group   Email: johns_at_ks.uiuc.edu
Beckman Institute              http://www.ks.uiuc.edu/~johns/
University of Illinois         Phone:  (217) 244-3349
405 N. Mathews  Ave              FAX:  (217) 244-6078 
Urbana, IL 61801, USA          Unix Is Good For You!!!
-- 
Theoretical Biophysics Group   Email: johns_at_ks.uiuc.edu
Beckman Institute              http://www.ks.uiuc.edu/~johns/
University of Illinois         Phone:  (217) 244-3349
405 N. Mathews  Ave              FAX:  (217) 244-6078 
Urbana, IL 61801, USA          Unix Is Good For You!!!