Hi Vijay, In addition to the suggestions you've already received, the pair_fit command in PyMol is also an easy way to align based on specific atoms. You could use the C-alphas of relevant active site residues, or atoms of the ligand itself, for example. Just be mindful of the bias introduced based upon your selection of atoms to align.
http://www.pymolwiki.org/index.php/Pair_fit Shane On Tue, May 26, 2015 at 8:41 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 > > >
