Dear Vijay, Your problem sounds like a job for LigAlign: http://www.pymolwiki.org/index.php/LigAlign
Regards, Dmitry On Tue, May 26, 2015 at 8:42 AM vijay srivastava <vijaytec...@yahoo.co.in> wrote: > Dear All, > > I want to superpose the nucleotide form one GTPase on to the nucleotide of > other GTPase in order to study > the interaction in the nucleotide binding pocket. I tried to superpose but > it is superposing on the basis of secondary structure as a > result both the nucleotides from two structutres are not properly > aligned. I want to superpose both the nucleotide, so that I will get the > matrix, which I want to apply on my desired strcuture and study the > interacting residues. > Do any one have the align program with you or any other program which can > solve this problem. > > waiting for your kind response > > regards > vijay > > >
