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

Wed Dec 11 12:17:36 PST 2013

Hi Tom,

This is a great answer. Thanks for checking out the code of pyMLP. You are always going above and beyond!

You're right about pyMLP handling only standard amino acids; my script would have to control for that.

The code does take some time to run. It isn't the fastest thing in the world. It takes me about 2 minutes to calculate a DX file for a 350-AA protein.

As for its utility for many users, I can only say that I've been looking for this functionality for years in open-source software and only recently found pyMLP after searching the literature and finding an old Italian paper. This functionality exists in SYBYL and it was at least one reason we have been hanging onto that license. It seems that the Schrodinger, Open Eye, and Accelrys suites also have this functionality (or something similar). I can't find any information about MOE. Adding it to Chimera may enhance its attractiveness as an open-source alternative to these commercial packages.

For now, I think I'll go with option 1. I know a little Perl and shell; I'm learning Python by crash course. Easy is good for now!

As an aside, it is important to remember that lipophilicity and hydrophobicity are often used interchangeably, but they are not synonyms. So the "render by attribute" using the Kyte-Doolittle hydrophobicity scale is a nice orthogonal check on pyMLP mappings.

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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From: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>
Date: Wednesday, December 11, 2013 2:46 PM
To: Darrell Hurt <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] Launch external program from Chimera python script?

Hi Darrell,

  The pyMLP code is a single 600 line Python file.

http://code.google.com/p/pymlp/source/browse/trunk/pyMLP.py

If you are familiar with Python you could probably turn that directly into a Chimera extension that could compute the lipophilic potential in Chimera without running a separate program, without reading PDB files or writing DX files.  To use a PDB model already opened in Chimera would require some knowledge of how to get the molecule data and then put it into the format pyMLP.py wants.  To use the calculated potential map without writing a DX files you'd need to know a bit about how to make a density map model in Chimera in memory.  These are pretty easy tasks but since we don't have good Chimera programming documentation we would need to show you the way.  Your first option of just running pyMLP and Chimera with a script would require less knowledge, and no need to use Python.  That would be easier.  Your second option is also easier than what I described above, because you still could just use PDB and DX files to pass data between pyMLP and Chimera.  I guess my advice would be to do the easiest approach first.  Then if that is somehow not convenient to use, do the next harder solution.  If that is not convenient to use, then do the still harder solution.

  If you think this is a valuable feature for many users, we could add it to Chimera.  My quick look suggests it would be a 1 day effort.  The pyMLP  code has a BSD license so there are no issues there.  The pyMLP code handles only standard amino acids, and I'm not sure if its limitations would cause trouble for users.

Tom

On Dec 11, 2013, at 11:15 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>> wrote:

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
31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559
Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<https://twitter.com/niaidbioit>
Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
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