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, 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. Thank you Appu On 13 January 2012 21:53, Ethan Merritt <[email protected]> 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 > > > >
