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]