Hi Darrell, Another problem with making this run within Chimera is that the calculation may take a very long time. Don't know without trying it. Tom On Dec 11, 2013, at 11:46 AM, Tom Goddard wrote:
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]" 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
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