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
