VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 08 2004 - 11:08:11 CDT

Dear VMD-L,
  I've just posted an updated set of VMD plugins based on the
most recent build I did on all platforms.

It will be a while before I can compile VMD or the plugins on
anything other than MacOS X, Linux (x86), Solaris, and Windows, so I felt it
prudent to post this update so that the well-tested feature improvements
can be used by people running VMD 1.8.2 until I can post a new set of plugins
down the road:
  http://www.ks.uiuc.edu/Research/vmd/plugins/182update4/

The update contains updates to several of the items in the VMD extension menu:
  - All VMD extensions menu plugins have been updated so their menus display
    more nicely on MacOS X.

  - 'vmdmovie' plugin is more failure tolerant, allows user to specify
    location of MPEG/AVI codec programs such as VideoMach/NetPBM if they cannot
    be found automatically

  - 'phiplugin' fix one of the built-in file validation tests
 
  - 'contactmap' beginning of a rewrite, bug fixes, and misc cleanup

  - New 'exectool' plugin provides a more fault-tolerant and
    resilient replacement for use of ::exec in other plugins.
    When the intended executable cannot be found, a GUI pops up
    and allows the user to specify the executable manually, etc.

The update contains various file reader/writer plugin improvements:
  - All binary file reader plugins now use improved byte-swapping
    routines that run up to 4 times faster than the old implementations

  - 'dcdplugin' now reads trajectory files at up to 175MB/sec for
    native-endianism files, and 120MB/sec for opposite-endianism files.

  - 'psfplugin' now reads PSF files produced by Charmm 31, in particular
    it handles files with the new "CHEQ" and "CMAP" features used with
    polarizable force fields.

  - 'psfplugin' now handles some unusual PSF files generated by CNS 1.1

  - a new 'gamessplugin' for reading GAMESS log files and reading in
    atomic coordinate data (work on reading e- orbital data is still ongoing).

  - new 'carplugin' for reading Insight II/Discover cartesian coordinate files

  - new 'mdfplugin' for reading Insight II molecules

  - 'cubeplugin' now reads unit cell data

  - updated pdbplugin/webpdbplugin to allow reading PDB files written with
    illegal atom index fields that overrun their field width (i.e. PDB files
    emitted from some Amber-related tools when working with structures that
    have > 99,999 atoms)

If you encounter any problems or find new bugs, please let us know.

Enjoy,
  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