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Pymol -> pairwise align wizard -> done - Cosmic Cats approve of this message On Tue, May 26, 2015 at 11:44 AM, Zhijie Li <[log in to unmask]> wrote: > Hi Vijay, > > I am not sure if I understand you correctly. If you want to align by the > two nucleotide in two GTPase structures, you can simply do it in COOT using > the “LSQ superpose” function. You need to fill in the chain id and residue > number only for the nucleotide and choose “all atoms”. Unless you want to > do this for more than 10 structures I think using COOT would be the most > simple way. For more than 10, you can use the CCP4 program LSQKAB to do it > in a batch format. > > If the two nucleotides have differences in atom naming or if some atoms > are missing, you may need to edit one of them (or model a “fresh” one), > although I guess for GTP/GDP this should not be a frequent problem. > > Zhijie > > > > *From:* vijay srivastava <[log in to unmask]> > *Sent:* Tuesday, May 26, 2015 8:41 AM > *To:* [log in to unmask] > *Subject:* [ccp4bb] Hi > > 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 > > >