From: Michael Swan
Subject: rmsd calculation for all atoms.
Dear all,
I am having a bit of trouble finding a program to do an rmsd
calculation and
give me the differences between all the atoms in the structures.
I have two structures which are identical in the sense that one is
the apo
protein and one is the bound structure. I would like to superimpose
them
using only one domain then output the rmsd values for all the atoms
or at
least individual residues. The structures are not completely
identical as
some extra residues were visible in the bound structure so I hope
there is a
program that can ignore those differences.
If anyone knows of a program that will do this calculation I would
much
appreciate hearing about it. There seem to be many programs that
will give
an average rmsd over the whole structure or just the region used for
alignment but I haven't found anything that will give me distances
between
atoms or residues that were not used in the alignment.
Thanks,
Mike.
If the domain is an entire chain, you could use Chimera's MatchMaker
tool to do the alignment:
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/matchmaker.html
It will report that RMSD for the atoms used for matching. To get the
RMSD for all atoms in common you would have to use the 'rmsd' command
and specify the parts in common:
http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rmsd.html
So if all of chain A and residues 12-20 of chain B were in common, then:
rmsd #0:.a:12-20.b #1:.a:12-20.b
If there were differences in the side chains (say some were
incomplete) then you might have to restrict the RMSD measurement to
the backbone (which you might want to do anyway):
rmsd #0:....@c,ca,n:12-2...@c,ca,n #1:....@c,ca,n:12-2...@c,ca,n
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
