pymol-psico
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STAMP for structural alignment
Have you considered adding a wrapper for the STAMP structural alignment method? I find it does a better job with some membrane protein structures that I've been working with (using through VMD's MultiSeq extension).
I wasn't able to find a pymol wrapper for STAMP through my own searching, but I may not be looking hard enough/in the right places.
http://www.compbio.dundee.ac.uk/software.html http://www.compbio.dundee.ac.uk/manuals/stamp.4.4/stamp.html
STMAP is licensed as GPL since version 4.4 (the most recent release).
My apologies for the very late reply.
I'm not familiar with STAMP yet. Pull requests welcome!