Hi Dan, gaps/insertions should be no problem for PyMOL's rms_cur command, as long as chain identifiers match (and all other atomic identifiers!).
See http://pymolwiki.org/index.php/Fit for a description of the matchmaker argument. Cheers, Thomas On 24 Feb 2015, at 16:30, D Bonsor <dbon...@ihv.umaryland.edu> wrote: > I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have > superimposed using Chain A. Several programs will produce the RMSD of Chain > A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain > B2, B3, B4... to Chain B1 when I have superimposed the structures relative to > Chain A. I have tried using Pymol though there are gaps/insertions so > rms/rms_cur will not work. Does anyone else have any other suggestions? > > Thanks in advance, > > Dan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
