[Chimera-users] Launch external program from Chimera python script?

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Wed Dec 11 11:15:34 PST 2013


Hi Chimera friends,

I am thinking of writing a script for Chimera that allows the user to map lipophilicity to the surface of protein. There are a few algorithms out there, but the easiest that I've found to use is "pyMLP":
http://code.google.com/p/pymlp/

I see two ways to do this:

(1) Write a wrapper script (shell, Python, etc.) to first run pyMLP to generate a DX file and then launch Chimera with its own script to generate the surface and do the mapping.

(2) Write a Chimera Python script to launch pyMLP to get the DX file, generate the surface, and do the mapping.

For my purposes, it might be easier in the long run to choose option 2, but that seems a little trickier starting out. Can you advise me on the best way to proceed?

Also, I know that you aren't looking to add new functionality to Chimera v1, but the generation of a lipophilicity map might be a nice feature to add to Chimera at some point and pyMLP seems relatively easy to package with Chimera…

Thanks,
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

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