Dear Ishan Would it be possible for you to use a fitting of the atoms of the ligand? I've done that with success before.
Hope this helps Folmer man. 16. dec. 2019 07.38 skrev Ishan Rathore <ishanrathor...@gmail.com>: > Hi, > > I am trying to compare multiple homologous structures of a protein, where > I am analysing the active site residues and the bound substrate/peptide. I > have used multiple methods for alignment in coot and pymol. Every > method gives a slightly different orientation in the active site. Based on > the analysis I am trying to propose a hypothesis for the catalytic > mechanism of the protein. But, I am a bit wary of getting biased with the > alignment if that supports my hypothesis. > > What are the parameters that have to be considered for a reliable > alignment? > What are the other Softwares available for alignment? > > > > Thanks and regards > Ishan > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
