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 Sent: Tuesday, May 26, 2015 8:41 AM To: CCP4BB@JISCMAIL.AC.UK 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
