[phenixbb] Off Topic: Calculating accurately RMSD

MARTYN SYMMONS martainn_oshiomains at btinternet.com
Thu Oct 2 07:28:12 PDT 2014

rmsd command in chimera allows you to specify atoms in alternate conformations - 
(https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html) there is a bit of a learning curve in getting the selection syntax right.
But I think it will only match the unique ones that you specify - not include all of a complete set of alternative confs,  which is maybe what you want.
rmsd takes the existing superimposition - match will do a superimposition
  all the best
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