VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 17 2006 - 11:37:34 CDT

Dear VMD-L,
  I've just posted VMD 1.8.4 on the web site for download:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/

I'll be posting the new Python libraries for the Linux builds and updating
various of the web pages over the next several days to match the new release.

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 1.8.4?
------------------------
  New Platforms Supported:
    o Support for Apple MacOS X 10.4 running on Intel based Macintosh computers
    o Support for IBM AIX 5.x on 32-bit and 64-bit POWER processors
    o Support for Linux running on Itanium based computers (e.g. SGI Prism)

  User Documentation Updates
    o Updated the URL listed for McKerrell's force field page in various
      plugin documentation.
    o Fixed missing 'clipplane color' subcommand in User's Guide
    o Updated User's Guide text about the MSMSSERVER environment variable
      for Windows.
    o Significantly expanded documentation pertaining to developing
      extensions and plugins in Tcl/Tk, Python, and C/C++.
       
  User Interface Changes
    o New '=' hotkey resets/recenters the view on the currently
      displayed representations
    o File reader/writer plugins are now listed in the graphical interfaces
      by a more descriptive name, the scripting interfaces continue to use the
      short/terse plugin names with no spaces in them.
    o The isovalue slider's range now updates when the selected isosurface rep
      is changed and/or the dataset is switched.
    o The Isosurface representation now includes a "step" control which
      makes it easy to display huge volumetric datasets at coarse resolution
      without resampling them first.
    o Disable selection text input field for volumetric reps (but preserve
      selection text value anyways), since this is not currently used.
    o Improved the default search location for 'explorer' on Windows 2000/XP.

  New Features
    o New "VolMap" extension for creating volumetric density and
      occupancy maps from atomic structure coordinates and trajectory data
    o New "AutoPSF" extension user interface helps automate structure
      building tasks in concert with the 'paratool', 'solvate',
      'autoionize', 'membrane', and 'psfgen' structure building modules.
    o New BioCoRE collaboratory extension interface allows an already-running
      instance of VMD to connect to BioCoRE to publish or display
      VMD views stored in the collaboratory.
    o New text viewing and editing extension
    o New MultiPlot extension takes provides built-in graphing and
      plot file export to PostScript and Xmgrace.
    o New NAMD Energy extension for calculating energies between atom selections
    o New NAMD Plot extension for plotting energies, runtime, memory use
      and other data from NAMD simulation log files.
    o New NAMD Graphical Interface extension for setting up and running
      NAMD simulations.
    o Added a "CrystalEyesReversed" stereo mode for projection systems that
      are one frame out of phase with the actual stereo sync pulse, such as
      the Christie Digital Mirage series projectors.
    o New "Beads" representation draws the bounding sphere for each selected
      residue, which is useful for displaying very large models at a coarse
      level of detail.
    o New "Shaded Points" Isosurface rendering mode for fast display of large
      volumetric isosurfaces
    o New Isosurface "step" size control allows easy subsampling of high
      resolution datasets when a crude subsampling method is sufficient
    o New "volN" atom selection keyword allows selection of atoms that
      correspond to specified voxel values for volumetric datasets
    o New "altloc" atom selection keyword allows selections on PDB structures
      that contain multiple conformations. VMD doesn't generate bonds between
      conformations with different identifiers.
    o New 'atomicnumber' and 'element' data fields are provided when structures
      are loaded from files containing unambiguous atomic element
      information. These new keywords can be used in atom selections.
    o New "Element" coloring mode will color atoms by their atomic element
      type, when available.
    o When atomic element information is available, VMD uses a periodic
      table lookup to determine atomic mass and VDW radii, if not it will
      guess using the old atom name recognizer heuristic.
    o New "measure avpos" command for measuring per-atom average positions
      over a trajectory
    o New "measure rmsf" command for measuring per-atom RMS fluctuations
      over a trajectory
    o New "measure sumweights" sum up mass, charge, or one of
      the other scalar floating point values efficiently.

  New and improved file import and export
    o New support for DCD files larger than 2GB on Microsoft Windows
    o New support for Charmm DCD files written with 64-bit internal offsets,
      as written by Charmm on x86_64 platforms when compiled with -i8.
    o New NetCDF-based file reader supporting AMBER 9 trajectories,
      and MMTK structure and trajectory files.
    o New Biograf (BGF) and extended BGF reader/writer plugins
    o New SPIDER volumetric image file reader for loading CryoEM maps
      and other volumetric data processed by the SPIDER software
    o New Situs volumetric map file reader loads EM maps processed by
      the various Situs tools
    o New MSMS surface file reader for loading already-calculated MSMS surfaces
    o New UHBD potential grid reader plugin
    o Updated PDB and WebPDB plugins parse atomic element and alternate
      location identifier fields, save all REMARK lines and unrecognized
      lines for query by the new 'molinfo top get remarks' command,
      and store the database and accession code for query by the new
      'molinfo top get database' and 'molinfo top get accession' commands.
    o Updated GAMESS plugin supports log files from newer GAMESS versions.
    o Updated PSF plugin can write out partial (no angles/dihed/etc) PSF files
      with bond records, for use by Situs and other tools.
    o Updated Mol2 plugin now writes mol2 files that are compatible with DOCK
    o Updated BRIX plugin now aligns correctly with new versions of VMD
    o Plugins using the fast I/O routines now use the user's Unix umask
      for file permissions when creating new files.
    o Fixed a bug in reading coordinates from GROMOS 96 files

  General Improvements and Bug Fixes
    o New built-in autodetection routine prevents problems with buggy ATI
      OpenGL drivers on Linux
    o Improved "color by volume" feature now automatically downsamples 3-D
      textures to fit within available texture memory on medium-range
      graphics boards when possible
    o New "serial" atom selection keywords provides one-based atom indexing
      for easier conversion of atom indices between VMD and other packages.
    o The movie maker plugin now supports user-defined movie types with a
      very simple scripting interface that allows researchers to develop
      very complex animations. The movie maker now works better when VMD
      is installed in a directory name that contains spaces and adds
      support for movie rendering with POV-Ray on Microsoft Windows.
    o Updated APBS plugin to emit the new syntax for the chgm, srfm, sdens,
      bcfl, calcenergy, and calcforce input file parameters to eliminate
      warnings with APBS versions 0.4.0 or newer.
    o Updated Multiple Alignment plugin fixes incorrect output from the
      qpair calculation on Microsoft Windows.
    o Force the Inform class to flush its output when sendmsg() is called,
      to prevent jumbled output when running VMD as a batch mode job with
      intermixed output from the VMD console, Tcl, Python, etc.
    o Added new 'gettimestep' command for efficient access to binary
      timestep data from Tcl.
    o Use boolean for the 'autobonds' suboption of 'mol new' so that values
      such as 1, on, true, yes, 0, off, false, and no all work rather than just
      1 and 0.
    o Fixed volumetric grid aligmnent for CCP4 and DSN6 plugins. They
      were scaled in each dimension by an extra factor of N/(N-1).
    o Fixed an atom selection leak in the AutoIMD plugin
    o Changed OpenGL version number tests to work correctly for video drivers
      that advertise themselves as OpenGL 2.0 or later
    o Fixed a potential atom selection crash occuring on "within"
      atom selections.
    o Print a useful error message when problems occur during Python callback
      registration
    o Added a new vmd_molecule (Tcl) and molecule (Python) callback
      to indicate when a molecule was created or its attributes were modified.
      Values for vmd_molecule(molid) are:
        0: deleted (identical to vmd_initialize_structure(molid))
        1: created (though no data is loaded at time of call)
        2: renamed
    o New Microsoft Visual Studio 2005 project for compiling VMD on
      32-bit and 64-bit editions of Windows XP

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