Hi Monica,
Calculate the mean B-factor of all atoms that making interactions with each ligand in monomer A and B. Use those means values as B-factors for each ligand respectively. Adjust manually the occupancies, in order the B-factors for each ligand to stay after refinement close to the above values. In order to calculate occupancies more precisely, it would help to have the un-liganded structure and thus the location of the water molecules in each binding site. If you have the above information you could refine water molecules and ligands simultaneously in the binding site and get accurate refined occupancies. George From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Monica Mittal Sent: Friday, April 18, 2014 1:04 PM To: [email protected] Subject: [ccp4bb] ligand occupancy Dear all I have a protein which is dimer having one ligand binding site in each monomer. I refined the crystal structure with ligand in both sites finally. I refined will full occupancy of 1 for ligands (same in both). But now i want to see is there any difference in the occupancy of both ligands in ligand binding sites of monomer A and B. Is there any way i can get any information about the occupancy of ligands in two monomers like one is binding more tightly than another so that i can get an idea about their differential binding contacts also. Thank you very much in advance. Regards Monica
