Dear Vijay, Have you try to use superpose in ccp4 ? In superpose it's possible to select exactly what you want (atoms, residues...) . In your case if you use only the atoms or the nucleotids that you want to be superpose, it could be ok.
Hope to help. Nicolas ________________________________________ De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de vijay srivastava [vijaytec...@yahoo.co.in] Envoyé : mardi 26 mai 2015 14:41 À : CCP4BB@JISCMAIL.AC.UK Objet : [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
