No, the question seems to be slightly different. While one can use
either CCP4's SSM or GESAMT to superpose 2 dimers, these algorithms
would balance RMSD between both chains and produce something optimal for
both chains. What is required, however, is optimal superposition on one
pair of chains (one from each dimer) but measuring RMSD on the other
pair of chains from same dimers. Nothing impossible in principle but no
corresponding option in general-purpose aligners (this requires
something like masks/selections for residues to superimpose and residues
to measure the RMSD on). If this were a common and frequent problem, we
could have it implemented in SSM/GESAMT.
Eugene
On 26/02/2015 12:47, Eleanor Dodson wrote:
Doesnt pisa give you some of this information? It lists all likely
homodimers and I think gives RMSD too
Eleanor
On 24 February 2015 at 22:00, Thomas Holder
<thomas.hol...@schrodinger.com <mailto:thomas.hol...@schrodinger.com>>
wrote:
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
<mailto: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.
