On Friday, January 13, 2012 09:07:07 am Appu kumar wrote:
> Firstly thanks to Robert Nicholls for making me aware of the software
> necessary for side chain RMSD calculation. I have installed and now going
> through manual to use it for exploiting the structural differences. Thanks
> a lot.
>
> Secondly, for Ethan Merritt, I am seeking the information for comparing the
> side chains RMSD for better comparison of structure. Please correct me if i
> am wrong, i want to elaborate more on what i am thinking. If we have refine
> the structure well so that issue of rotamers are fixed
Sorry, I don't know what you mean when you say "the issue of rotamers are
fixed".
> , then it is
> possible to take the advantage of side chain orientation for correctly
> understanding the trivial differences between homologous proteins and such
> differences harbouring good piece information for understanding protein
> structure-function relationship. Any kind of suggestion would be highly
> appreciated.
Let me put it this way. Suppose you were reading a paper about someone
else's structures. Which of these two statements would be more useful:
1) The RMSD for sidechain atoms between apo and holo was 0.678 Å.
or
2) Only two residues exhibited a significant change of conformation:
the Asn XXX carboxamide flipped 180 degrees allowing ND to act as
H-bond donor to ligand atom FOO; the Lys YYY sidechain occluded
the ligand binding site in the apo structure but extends into the
solvent when the ligand is bound.
Your comparison apparently involves a pair of homologs rather than a
pair of holo/apo structures, but I suggest to you that RMSD is even
more useless in this case. For residues where the two sequences are
not identical, how do you even calculate an RMSD for sidechain atoms?
Ethan
>
> Thank you
> Appu
>
> On 13 January 2012 21:53, Ethan Merritt <merr...@u.washington.edu> wrote:
>
> > On Friday, 13 January 2012, Appu kumar wrote:
> > > Dear ccp4 users,
> > > Would you please guide me how to calculate
> > > the RMSD of side chains alone without considering C-alpha backbone.
> > > Is/are there any program/programs availble which do this job. I want
> > > to know the RMSD of side chains for protein comparison.
> >
> > What is the question that you are trying to answer?
> > If you are going to disregard the mainchain position, then
> > I would guess that you'd be better off comparing rotamer
> > classes than comparing coordinates.
> >
> > Ethan
> >
> >
> > >
> > > Thank you in advance.
> > > Appu
> > >
> >
> >
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
