[Chimera-users] RMSD script

Ruth Nelson Ruth.Nelson.180 at nd.edu
Wed Nov 18 09:38:04 PST 2015


I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from
each PDB file to every other PDB file in that matrix. When I do this in the
command line of Chimera, I type something like "match #0 #1" or "match #0
#2" for each of my PDB files, but I would like to automate this process so
that it does not take as long. I have hundreds of files and they are all
are named similarly (file_1.pdb, for example) but they are not numbered
consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If
possible, I would like the RMSD values to be output into a CSV file so that
I can open it in excel.

I have very little experience writing scripts and no idea where to begin to
write this one, so I would greatly appreciate any help. I have been reading
some of the responses given to other people regarding similar scripts, but
I am having a hard time translating that to what I would like to do.

Thank you very much,
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