[Chimera-users] BioPython in a Chimera Python script; PDBio?

[Hurt, Darrell (NIH/NIAID) [E]]

Hi Chimera friends,

I've been trying to install BioPython into the Python interpreter embedded within Chimera. I've been following the guidelines posted a couple of years ago:
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000807.html

This works up to a point for me. I'm using Mac OS X 10.8.5 with MacPorts installed. I'm trying to install BioPython 1.63:
http://biopython.org/wiki/Download#Installation_Instructions

The "build" process starts to work, but gets hung up with the error "xcrun: Error: failed to exec real xcrun. (No such file or directory)". It seems to be referencing "/Developer/SDKs/MacOSX10.6.sdk", which does not exist in recent versions of Xcode. I've been able to install the 10.6 frameworks into both Xcode 4.6.2 and Xcode 5.x, but that still doesn't work. I manually installed the MacOSX10.6.sdk from Xcode 4.2 into the appropriate location, but still no luck.

I'm using BioPython because I want to pull some information out of the PDB headers. I was able to use PDBio as described in this discussion:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001291.html

But the "dictionary" entries "keyed by record type" need additional cleanup/parsing before I can use them (which is why I wanted to use BioPython).

Is this just a case of Apple not building in enough backwards compatibility? Or is it something that Chimera needs to fix?

Do you have any additional suggestions for me about "PDBio"? The fields I want are the DOI and title information.

Finally, is there an analogous "EMDBio" for EMDB records?

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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