Hi vijay, I think the pymol-based program “legalign” will do what you want: http://compbio.cs.toronto.edu/ligalign/ <http://compbio.cs.toronto.edu/ligalign/>
Hope this can help, Marco > Il giorno 26/mag/2015, alle ore 05:41, vijay srivastava > <vijaytec...@yahoo.co.in> ha scritto: > > 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 > >
