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Hello all, I am refining a structure (using REFMAC currently, but have tried with phenix as well) with a ligand with alternate conformations. I have added each conformation to the pdb file with 0.5 occupancy and named as A and B and have been able to refine that. The problem is only two atoms are in an alternate conformation, while I have 17 atoms total in my ligand (which are positioned the same - i.e. a carboxyl and sugar ring I only see density for one conformation). After a round of refinement with A and B conformations of the entire ligand, I have two conformations of my ligand (one shifted relative to the other in the density) in which the second conformation does not fit into the density, except for the 2 atoms of concern. If I refine with just the two atoms that are different labelled as partial occupancy A and B, a bond is broken in my main (or rather 'productive') ligand binding conformation, and the bond remains with the 2nd conformation. My question is should I make a LINK in the cif file for this ligand to restrain the bond I want to keep? Is that the best way to go about this? I initially tried putting both conformations of the two atoms into the CIF file, but that is not correct as the CIF file thinks that they are both fully there (i.e. no occupancy in the CIF file) (used phenix.elbow to generate CIF files). Any suggestions on how to move forward? Thanks in advance, Kelly ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *******************************************************