Hi James,

On the pymol-wiki there is a script called findseq (http://pymolwiki.org/index.php/Findseq)
That does what you want (or at least the first part of your request)

Best regards,

2014-04-05 13:29 GMT+02:00 James Starlight <jmsstarlight@gmail.com>:
Dear PyMol users!

I'm learning of the python scripting for the solution of typical structural bioinformatics problems. This time I'd like to integrate in pymol simple script which will search for the selected motifs (just several amino acids situated in adjacent positions along the sequence) and marked selection data assuming that I'm working with  ensemble of homologue proteins having common motifs. Could someone provide me with the example of such script included pymol syntax in code? During further steps I'd like to improve such script for searching  of motis situated in adjacent space position in 3D pdb structures but not in its sequences.

Thanks for help,



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Folmer Fredslund