[Chimera-users] MatchMaker with betapeptides

Elaine Meng meng at cgl.ucsf.edu
Sat Nov 29 14:35:30 PST 2014

Hi Russell,
Oh, I realize now what you meant by beta peptides… I had misunderstood it as beta-strands.  I believe Matchmaker only works on standard (alpha-amino acid) peptides; for beta-peptides, you would have to use the “match” command.

On Nov 28, 2014, at 10:32 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Russell,
> I don’t know about the “incompatible” message ( you may need to use Help… Report a Bug and attach a session with some example structures that give this message), but there is a MatchMaker option "Further restrict matching to current selection” to limit the calculation to selected residues:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
> In the mmaker (matchmaker) command, you could do it by specifying only the desired residues:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict>
> Matchmaker and Match are both pairwise.  Even though you can choose multiple structures to match in the MatchMaker dialog, each is only matched to the single reference structure. So correspondingly, you would just need to use the command multiple times, one for each pairwise match; just keep using the same reference structure.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Nov 27, 2014, at 11:22 PM, 러셀 <rwdriver at kaist.ac.kr> wrote:
>> 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,
>> Russell
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