VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 25 2006 - 23:51:22 CDT

Dear VMD-L,
  I've just posted VMD 1.8.5 on the web site for download:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.5/

In addition to the officially-supported binaries, some unofficial RPM
and alternate MacOS X builds are also available, with more coming as
time allows.

For those of you that haven't seen the beta versions we've made available,
here's the list of new features and improvements found in this version:

What's new in VMD 1.8.5?
------------------------
  General Improvements
    o MacOS 10.4 versions for PowerPC and Intel processors support
      quad-buffered stereoscopic display on Macs with Quadro 4500
      graphics cards (or similarly capable hardware).
    o New MultiSeq 2.0 multiple sequence alignment plugin replaces the
      multiple alignment plugin, and allows both structure based sequence
      and pure sequences to be aligned and analyzed
    o Support for VRPN 7.03, lower cost HDAPI-based haptic devices

  User documentation updates
    o MultiSeq 2.0 documentation has been added
    o APBS plugin docs include a short tutorial on coloring solvent
      surfaces by potential
    o Significantly expanded documentation for users interested in developing
      extensions and plugins in Tcl/Tk, Python, and C/C++.
    o Minor improvements and corrections to the VMD User's Guide,
      added documentation for new commands and environment variables.

  User interface changes
    o "RWB" is now the default color scale (previously "RGB")
    o New min/max range controls for isosurface representation isovalue slider
    o The materials menu is now populated with a much larger set of
      materials by default.
    o OpenGL Shading language compiler diagnostic errors are now printed
      only when the VMDGLSLVERBOSE environment variable is set.

  New representations and display features
    o NewCartoon representations now draw nucleic acid structures with
      ribbons for the backbone and cylinders for each nucleotide
    o Significant improvements for display of nucleic acids using the existing
      NewRibbons and NewCartoon representations
    o Dynamic reclalculation of bonds can now be set for several additional
      atom-oriented representations, for use with trajectory playback
    o Pick points can now be created for user-defined graphics, to allow
      the creation of completely customized graphics and behaviors using
      the scripting interfaces.
    o The built-in color table and menus now contain 32
      user-modifiable base colors rather than the old limit of 16.
    o Atom labels can now be displayed with user defined format strings,
      and with a defined offset from the atom coordinate.
    o Added new "RGryB" and "BGryR" color scales for use when coloring
      by potential on white backgrounds
    o New VMDVMDMACENABLEEEXTENSIONS environment variable enables
      performance-oriented OpenGL extensions which trigger bugs
      on some Mac systems.
    o New VMDSHEARSTEREO environment variable enables an alternative
      perspective projection mode for improved stereoscopic display
    o New VMDIMMERSADESKFLIP environment variable enables a special
      reversed/reflected stereo projection mode for use with experimental
      displays based on LCD panels, phase plates, and beam splitters.

  New analysis commands
    o New 'measure dipole' command for calculating dipole moments
    o New 'measure gofr' command for calculating radial pair distribution
      functions
    o New 'mol reanalyze' command allows one to force VMD to completely
      re-analyze the molecular structure due to changes in atom names,
      residue names, bonding/topology, etc. This is intended to be used by
      structure building tools and other special applications where one wishes
      to change the structure on-the-fly.

  New and improved plugins and extensions
    o New MultiSeq 2.0 multiple sequence alignment plugin replaces the
      multiple alignment plugin, and allows both structure based sequence
      and pure sequences to be aligned and analyzed
    o New BioCoRE collaboration plugins for chatting,
      remote file system access, remote job submission, and VMD state exchange
    o New "Virtual DNA" visualization plugin can display a graphical
      representation of DNA according to its helical parameters (no atomic
      structure)
    o New "g(r)" graphical interface for radial pair distribution
      function calculation and plotting
    o New IR spectral density calculation and plotting tool
    o New representation cloning visualization plugin makes it easy to
      copy a set of representations from one molecule to another
    o New Palette Tool visualization plugin displays active colors
      and materials, for test rendering and printing
    o Molefacture plugin now allows structures to be built from scratch using
      a library of fragments and residues
    o New Salt Bridge plugin finds salt bridges that form over a trajectory
    o New CGTools plugin for converting between coarse grain
      and all-atom models
    o New 'NavFly' mouse-based flying camera navigation plugin
    o Mutator plugin now includes support for free energy perturbation
    o APBS plugin now includes a mobile ion editor, and
      supports job remote execution
    o NAMDEnergy plugin now supports remote job execution
    o Extended the exectool plugin with support for remote job submission
      through BioCoRE
    o Improved the clipping plane tool user interface
    o Improved Color Scale Bar plugin now has better range controls,
      improved behavior with white backgrounds, and generally more robust.
    o Improved Ramachandran plotting plugin includes a new 3-D time averaged
      histogram display feature.

  New and improved file import and export
    o New VASP plugins read atomic configurations, trajectories,
      charge density and electron localization function volumetric grids.
    o AMBER file readers now convert to/from elementary charge units
    o Improved Gromacs plugin now reads TRJ trajectory files
    o Improved column alignment in mol2plugin mol2 file writing routines
    o Improved LAMMPS plugin now reads more structure data out of trajectories

  Bug Fixes
    o Fixed a potential crash when 'measure contacts' was used with a
      very very small distance parameter, on very large structures
    o Fixed a potential crash in the labels window when molecules were deleted
    o Fixed a memory leak in the atomselect 'moveby' subcommand
    o Fixed a potential crash in the 'atomselect macro' command
    o Fixed the state saving script so that it correctly saves and restores
      the user-defined clipping planes. Also made the state loader more
      robust so that any color settings errors don't abort the loading
      process, and will continue on with remaining color settings.

Known bugs
----------
  Visit the VMD page for information on known bugs, workarounds, and fixes:
    http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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