[Chimera-users] MatchMaker with betapeptides

러셀 rwdriver at kaist.ac.kr
Thu Nov 27 23:22:44 PST 2014

Dear Chimera users,
I would like to use the MatchMaker utility to superimpose a family of beta peptide conformers calculated through Xplor-NIH.  Unfortunately, MatchMaker does not recognize these molecules and tells me the "chains are incompatible".  Furthermore, I would like to specify that only certain residues in the beta peptides be used in the global alignment.
I know how to match specific selections in 2 models through the Match utility using the command line (sel #0:1,2,3,4,5 at CB,N,C,CA #1:1,2,3,4,5 at CB,N,C,CA and then match sel) but I am unsure how to superimpose all of the models at the same time.  For instance: models #1-20, residues 2-8, atoms C, N, CA, CB.
If anyone could offer me help on the appropriate syntax I would be grateful.
Thank you and best regards,
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