I would suggest biopython. http://combichem.blogspot.com/2013/08/aligning-pdb-structures-with-biopython.html
On Tue, May 26, 2015 at 10:25 AM, Dimitry Rodionov <d.rodio...@gmail.com> wrote: > 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 >> >> >>
