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Hi Kelly, since you mentioned you tried refinement in phenix.refine: I guess I know what the problem is, but I wouldn't tell before I'm sure. Could you send me the two PDB files: before and after refinement (to my email, not to the whole bb), and specify which residue/ligand is in trouble? If you send the data as well, then that would increase the chances of finding the solution to this -:) Pavel. On 1/20/10 5:33 AM, Kelly Daughtry wrote: > 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 > ******************************************************* >