Well - if you know how the residues match then LSQKAB can compare all atoms and will give you RMSDs for matching pairs. SSM machos things according to secondary structure, and PISA analyse structure so you can compare the chemistry of the matched pairs.. But there is no easy option that I know of - some of the analysis is going to be subjective.. Eleanor
On 1 Apr 2013, at 15:07, Rex Palmer wrote: > We have two refined protein structures of similar proteins. There are > differences in the amino acid sequences however and also in the bound waters > and ligands. > Does anyone know of a program which we could use in order to quantify the > structural differences associated with these factors? > > Rex Palmer > http://www.bbk.ac.uk/biology/our-staff/emeritus-staff > http://rexpalmer2010.homestead.com
