VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 16 2005 - 00:09:04 CST

Dear VMD-L,
  I've just posted VMD 1.8.3 on the web site for download:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.3/

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 1.8.3?
------------------------
  User Documentation Updates
    o Source code documentation is provided online and is updated nightly.
    o Extensive updates to the VMD Tutorial have occured for the new version

  User Interface Changes
    o New controls and text commands for changing label text size
    o The defalt behavior of the isosurface representation slider is to
      calculate an isosurface with half as many samples per axis while the
      slider is being dragged, providing a much faster interactive rendering
      rate, followed by a full resolution isosurface computation when the
      slider is released. In cases where it is desirable to get a full
      resolution isosurface as it is being adjusted, holding down any of
      the shift/ctrl/alt keys will force VMD to calculate the isosurface at
      full resolution even while dragging the slider.
    o Isosurface reps are automatically created (with box) when volume data
      is loaded into a new molecule (rather than lines).
    o The color scale range can be customized for the "Index" coloring method

  New Features
    o New APBS electrostatic potential interface plugin
    o New Camera Navigator plugin allows the user to fly the camera
      using the keyboard in perspective projection mode.
    o New Clipping Plane plugin provides a simple interface to manipulate
      the 6 user-defined clipping planes to one, all active, or all molecules.
    o New Multiple Alignment plugin performs sequence and structure alignments
      on molecules loaded in VMD.
    o New PMEpot Particle Mesh Ewald potential map calculation plugin
    o New graphical interface for Solvate plugin
    o New ViewMaster plugin provides an easy-to-use interface for
      managing multiple molecular views, saving them, and switching between
      them.
    o New "Volume" coloring method, for use with electrostatic potential maps,
      and other volumetric datasets. Requires OpenGL 1.2 3-D texture mapping.
    o New "NewCartoon" secondary structure representation draws better
      looking structures than the original cartoon representation and
      animates faster for trajectory playback.
    o New "measure sasa" command to measure solvent accessible surface area
      for an atom selection.
    o New "color restype" command to override the default assignment of
      residue types used for coloring by residue type.
    o Windows version of VMD now supports MSMS surface representations
    o Windows versions of VMD now support 3-D texturing used by the
      "VolumeSlice" representation, and the new color by "Volume" feature.
    o New "display cachemode" command and matching Display menu controls,
      enable whole-molecule display list caching in VMD, which can yield
      significant performance improvements when rendering over a network
      or on tiled display systems, or when rendering large static structures
      with high triangle counts such as isosurfaces.
    o New "display rendermode" command and matching Display menu controls
      provide a nicer way to switch into and out of the special
      alpha-blended transparency and GLSL rendering modes.
    o Preliminary support for OpenGL shading language (GLSL).
      VMD shaders will continue to be updated over time, the first
      implementation is now workable, though it has various limitations.

  New and improved file import and export
    o Significantly improved Tachyon and POV-Ray output for MSMS surfaces,
      NewRibbons, and other triangulated surface geometry.
    o All molecular geometry can now be exported to external renderers that
      support triangle primitives.
    o New Wavefront OBJ renderer format for use with tools such as Maya
    o New DLPOLY formatted HISTORY file reader plugin
    o New Insight II/Discover "car" reader plugin
    o New LAMMPS molecular dynamics trajectory reader plugin
    o New PQR file reader/writer plugin
    o New SYBYL "mol2" reader plugin
    o New Tinker "arc" reader plugin
    o New Molecular Discovery GRID volumetric map reader plugin
    o Significantly improved the Amber 7.x parm plugin with rewritten code
    o Updated Charmm coordinate file reader plugin addressing a bug
    o Updated Gaussian Cube plugin to read non-orthogonal unit cells
    o Updated PSF structure file reader plugin to read PSF files
      created by CNS 1.1
    o Updated XYZ plugin to parse files containing atomic numbers rather
      than string-based atom names.
    o Significant DCD trajectory reader performance improvements
    o The DCD trajectory reader/writer plugin has been udpated to fix
      a byte swapping problem on Charmm trajectories containing fixed atoms,
      and now writes files in Charmm/NAMD format by default including
      unit cell information.
    o Updated the DX reader plugin to fix a potential problem reading
      grid lengths, and to use friendlier volume dataset names
    o Updated the Gromacs readers to allow periodic cells with zero-length
      periodic cell dimensions
    o Updated brixplugin, ccp4plugin, edmplugin, and fs4plugin fixing a bug
      in handling non-orthogonal cells.
    o All plugins now use common byte swapping code for greatly increased
      performance reading opposite-endian binary files. In actual use,
      this results in byte-swapped DCD trajectory reading performance of
      up to 294MB/sec on high-end workstations, with medium-range
      machines achieving 100MB/sec from local disks.

  General Improvements and Bug Fixes
    o 20-fold performance increase when rendering volume slice representations
      on most graphics accelerators.
    o More than tripled the peak read performance large trajectory
      files using the "waitfor all" option compared with previous versions.
    o The 'vmdmovie' plugin now generates movies much more quickly
      due to new features implemented by the Snapshot and InternalTachyon
      renderers and improved image format conversion logic.
    o The 'vmdmovie' plugin now supports the use of POV-Ray for ray tracing
      of movies
    o Numerous AutoIMD improvements make it more usable on local workstations
      and more easily configurable to local clusters and queueing systems.
    o Atom selection 'set' operations now perform at peak speed without
      the need to disable display updates or other performance tricks.
    o Significantly improved the 'points' isosurface representation,
      selected better defaults for the isosurface representation.
    o Atom selection performance improvements for "name" and arithmetic
      evaluation selections.
    o Better range checking when writing PDB files from molecules in VMD
    o Eliminated string copy of residue indices
    o The Windows joystick code now emits user key events for button presses.
    o The "FPS" indicator's color can now be changed in the Color window.
    o Corrected the position of user-defined clipping plane origins
    o Faster picking performance over networks
    o Bond search code now tolerates wildly out-of-scale atom coordinates and
      handles unusual situations much better. Minimal error messages are
      printed now, and crashes should not be possible now.
    o The 'delete trajectory frames' GUI now behaves as one would expect
      rather than the strange frame selection logic used in past versions.
      The stride parameter now specifies the frames to _keep_:
      deleting 0 to 9 with a stride of 4 will keep frames
      0 4 8, instead of the old behavior 1 2 3 5 6 7 9.
    o The 'vmd' startup script for Linux now correctly auto-detects the
      appropriate binary to run on x86 and x86_64 Linux distributions.
    o Enhanced the shutdown process to allow plugins and scripts to
      terminate cleanly if they have callbacks and such.
    o Updated Contact Map and Timeline plugins with improved user interface
      code. Cleaned up the user interface.
    o Improved built-in help for various text commands
    o Fixed problems that occured with psfgen and very long filenames 

-- 
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