Tutorial

Run external applications from within Bioclipse

A feature of Bioclipse is the general ability to execute third party applications on BioResources. As an example, I will here demonstrate how to connect the excellent molecular visualization tool Pymol to Bioclipse and connect it to right-clicks on molecules.


If you have not downloaded and installed Pymol, do it now. Instructions and resources can be found at http://pymol.org Note the directory where you install Pymol; it will be needed later.


Go to the menu alternative: “Help -> Preferences...” and click on Applications paths to reveal the window below:



Here you can specify external programs that will be run, and the file extension that it is capable of handling. Pymol is provided as a reference external application, and will most probably need customization to operate.



Now, click on “Edit” to open the following dialog:

In the Name field you may specify a name to identify the application, and will appear in the context menu when a file matching the above specified file extensions is right-clicked.


The Extensions are what file extensions the external application should be available for. If multiple file extensions, they are separated by comma.


The Path field specifies where the application is located on your harddisk. Click “Browse” and locate the external application. For this tutorial, locate the Pymol installation directory and select “pymol” from within it. Click “OK” and see the Path updated for the new location.


Click “OK” in the Preferences window.


Now, right-click a PDB-molecule (ending with .pdb) in the BioResource navigator and note the action “View in Pymol”.

Test running the Action. Pymol should open and display the selected PDB-file.



Troubleshooting

It the external application doesn't start, it is most likely due to a misconfiguration in the Preferences settings. Look at the command and any error messages displayed issued in Bioclipse Console. Try to copy the command between the apostophes and paste it to the command line.

When you have figured out the error, go to the Preferences and update the information e.g. if the location was incorrect or misspelled.

Ola Spjuth [ola(AT)bioclipse.net]