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

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Tue Jan 7 11:55:16 PST 2014

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:

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:

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:

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?


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
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