Hi Jordan, use the "pepseq" selection operator:
select align_1, protein_1 and pepseq YYDFGHSFG select align_2, protein_2 and pepseq YYDFGHSFG align align_1, align_2 Cheers, Thomas Jordan Willis wrote, On 07/23/14 21:58: > Hi, > > I have a really just awful way of doing this and was wondering if there is a > pymol solution that would make it easier. > > Here is the problem. > > Given two protein sequences, align their corresponding amino acids. The > position of each of the strings is not known, just the sequence. > > Ex. > > Protein 1 - XXXXXXXXXXXXXXYYDFGHSFGXXXXXXXXXXX > > Protein 2 - - XXXXXXYYDFGHSFGXXXXXXXXXXX > > > What I would like is to select the sequences (pseudocode obviously). > > select align_1 ,protein_1 and YYDFGHSFG > select align_2, protein_2 and YYDFGHSFG > align align_1, align_2 > RMSD is X.XX > > Does this functionality exist? > > Jordan -- Thomas Holder PyMOL Schrödinger, Inc. ------------------------------------------------------------------------------ Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
