VMD Plugin Library

VMD 1.8.6 Plugin Update 1, Released 9/21/2007

This is the first plugin update for VMD 1.8.6. The release includes new and improved molecule file reader/writer plugins, as well as improvements to several of the GUI extension plugins included with VMD 1.8.6.

New features and improvements in this plugin release:

  • vmdmovie: Applied corrected the transparent surface rendering for movies made using Tachyon. Also fixed the behavior of the ::makemovie method intended for use by external scripts etc.
  • pmepot: Add ability to update selection for each frame.
  • psfgen: Look up atom type id when writing CHARMM format psf file, allowing an X-PLOR format psf file to be read and translated to CHARMM format as long as the required topology files are loaded.
  • pbctools: PBCTools plugin version 2.1 updates from Olaf Improved error handling. Added -verbose option to wrap, unwrap and join. Added -check option to pbcget: checks the cell parameters for validity. Added generic pbcwrap_coordinates function to wrap coordinates into a unit cell around another coordinate. First implementation of pbc join.
  • molefacture: Fix problem with running molefacture multiple times in one vmd session
  • cgtools: Added in the ability to determine the bond cutoff information from the all atom model. Before, it was done using a cutoff. Now the user can choose to use the cutoff distance, but it uses the information from the all atom model by default
  • atomedit: Use Courier as the default fixed font.
  • dowser: Fixed a bug that occurred when the top molecule was a map.
  • molefacture: Allow inversion of chirality and add a button for it Also, add ability to save mol2 files from molefacture gui

New and improved molfile plugins

  • mol2plugin: several memory allocation/deallocation bugs similar to bgfplugin and xbgfplugin, as well as some mismatched new/delete/malloc/free usage.
  • Fix identical memory leaks in the bond reading codes for bgfplugin and xbgfplugin.
  • Added Jan's fix for a memory leak in part of xbgfplugin We'll need to verify this and also likely check the bgfplugin just to make sure it doesn't contain the same problem.
  • situsplugin: Implemented situs writer.
  • ccp4plugin: updated source comments.
  • edmplugin: Fixed volumetric grid aligmnent for the X-PLOR map reader. It was scaled in each dimension by an extra factor of N/(N-1).
  • dxplugin: Print line containing dataname at the end of dx file. Also, remove any quotes in dataname before printing it.
  • dxplugin: Fixed DX writer. It was printing the the axis size instead of the grid spacing in the header.

Installing the new plugins:

The link below will download the latest directory of VMD 1.8.6 compatible plugins for all of the supported platforms. We intend to provide a new "updater" plugin soon. Until the updater plugin is ready, you may manually unpack this plugin distribution into a directory on your system. Once unpacked, you can use the new plugins either by replacing the plugin directory in your installed VMD distribution, or by adding commands similar to the following examples, to your personal .vmdrc or vmd.rc file. In order to utilized updated GUI extensions, you must replace the plugins in your installed VMD distribution. If you only want updated molecule file plugins, the .vmdrc/vmd.rc based plugin update method is sufficient.

Unix and MacOS X .vmdrc additions: 

menu main on
# Load the molecule file reader plugins from ~/plugins/....
# This command will evaluate to something like:
#   vmd_plugin_scandirectory   /users/johns/plugins/SOLARIS2/molfile   *.so
vmd_plugin_scandirectory [file join $env(HOME) plugins [vmdinfo arch] molfile] *.so

Windows vmd.rc additions: 
menu main on
# Load the molecule file reader plugins from c:/plugins
vmd_plugin_scandirectory   c:/plugins/WIN32/molfile   *.so

Newest VMD 1.8.6 plugins for all platforms

Note that when unpacked, this archive will consume approximately 70MB of disk space. Once unpacked, you may delete the subdirectories which correspond to architectures you don't need or use.

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