MultiMSMS VMD plugin

The MultiMSMS VMD plugin caches the Solvent Excluded Surface computed by MSMS to speedup the animation of a sequence of frames.

The first loop through the full trajectory creates, in a cache directory, one file (called msms_???_??????.tri) for each frame and each representation of the top molecule.

Subsequent runs simply display the surfaces reading them from those files instead of recomputing them every time.

Download

The current plugin version is 1.0.3 (20-apr-2006) and is available as multimsms1.0.zip (Windows friendly) or multimsms1.0.tar.gz (Linux friendly).

The plugin is architecture neutral and has been tested using VMD 1.8.3 on Linux Suse 10 and VMD 1.8.4 on WinXP SP2.

Check the version history for change descriptions.

If you do not have MSMS installed, download it from the Michael Sanner software site.

Installation

1. Decompress the archive and copy the extracted multimsms1.0 directory in the VMD plugins/noarch/tcl directory or somewhere else
2. Depending on the location chosen:
   1. If the plugin has been installed in the VMD plugin directory edit the provided vmdrc-additions file and delete the line: lappend auto_path /home/mvalle/w/VMDplugin
   2. If the plugin has been installed somewhere else, for example in the directory {your_plugin_dir}, edit the provided vmdrc-additions file and change the line: lappend auto_path /home/mvalle/w/VMDplugin to: lappend auto_path {your_plugin_dir}
3. Move the provided vmdrc-additions file to your home directory renaming it to .vmdrc or append it to an already existing .vmdrc file in your home directory, or on Windows append it to the vmd.rc file found under the VMD installation
4. If needed install the MSMS executable in a place of your choice. Then be sure the MSMSSERVER environment variable is set and points to the MSMS executable
5. Optionally define the MULTIMSMS_CACHE_DIR environment variable to point to a local directory to be used to store the cached files

Usage

1. Load a molecule. Be sure it is the Top molecule.
2. Create a representation for each part of it that should have a surface computed. The representation should not be MSMS.
3. Go to the initial step you want to visualize.
4. Open the plugin GUI (Extensions > Multi MSMS).
5. Select the cache directory. If no selection done, the value of the MULTIMSMS_CACHE_DIR environment variable, if set, or the current directory is chosen as the cache directory.
6. Optionally delete any previous cached file using the "Clear cache" button.
7. Optionally set the "Probe radius" and "Density" values for the MSMS program.
8. Optionally set the "Material" to be used for the generated surfaces
9. Enable processing using the "Enable MSMS results caching" toggle.
10. Run the animation. For any uncached step the plugin builds the corresponding cache file. If instead a cached step is found it is reused and not recomputed.
11. Exit from the plugin using the "Dismiss" button. This button disables also the result caching, but does not delete the cached files

History

Version 1.0.3 (20-apr-2006)

Added a better plugin installation command.

Version 1.0.2 (26-jan-2006)

Handled the case when MSMS sometimes exits with an error, but the result is valid.

Version 1.0 (30-nov-2005)

Initial release.

Limitations and To Do list

• Missing validity controls (checks if no molecule loaded, no atoms resulting from atomselect, etc.).
• The surfaces are colored only by the component number.
• The mouse is frozen during reloading.
• A surface update when changing material should be added.
• More flexibility needed for selecting the input molecule: currently it should be the top molecule only.
• The resulting surfaces should be put in a new molecule, not back in the top molecule.

Contact

Contact me for any problem or request related to the plugin.