Hello all - 

I'd like to share with you this script that I recently added (with Troels' help) to the PyMOL Wiki.

http://www.pymolwiki.org/index.php/Elbow_angle

Given a PyMOL object containing an antibody Fab fragment complex, light and heavy chain IDs for the Fab, and residue numbers for the boundary between variable and constant domains for each chain, the script will output the elbow angle of the Fab complex and optionally draw a representation of the vectors used to calculate it.

It's under version control in the Pymol-scripts-repo, and any suggestions and/or fixes are welcome.

Please note that elbow_angle requires transformations.py by Christoph Gohlke and com.py by Jason Vertrees, both of which are also available in the Pymol-scripts-repo.

Cheers,
Jared

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Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Ave MSB 398
New York, NY 10016
212-263-7898