You are right that refining occupancy and B value at the same time cant be done with REFMAC, and probably wouldnt work anyway at 2.9A
However, if you set the ligand occupancy to 0.7 say, and refine the residue B factors, the occupancy should not be set back to 1.0. It certainly isnt in the local version of REFMAC. You can judge to some extent what occupancy gives the cleanest map by inspection. But at 2.9A the correlation between B and occupancy is very high and it wilnswer. l be hard to get a definitive answer. Eleanor On Wed, 13 Jul 2011 10:31:59 -0500, dhurjati putcha <antharvaah...@gmail.com> wrote: > Dear CCP4ers,ncy and B value > > While trying to refine a protein-ligand structure (reso=2.9A) I notice that > the density (2Fo-Fc)for the ligand is discontinuous. I also notice that the > density for the residues in the ligand binding pocket (LBP) is also very > feeble. And when I refine the ligand occupancy the density for the ligand > appears and covers almost all the molecule, and the occupancy refines to > <1.0. > > However, I cannot refine the occupancy/B factors for the LBP residue side > chains because the occupancy stays at 1.0 (and if I change it manually, it > returns to 1) and the B factors (group & individual) remain close to the > average for the remainder of the molecule. If I omit the LBP residue side > chains, I get some Fo-Fc density suggesting that these side chains are > real. > > > Is there previous evidence for such phenomena suggesting multiple > conformations/dynamics/loose binding? Is there a way to quantify the > dynamics associated with the side chains (as with the ligand where the > occupancy is <1.0) so I can argue it out with potential manuscript > reviewers? The R-factor/R free #s (22%/19%) suggest that the refinement is > nearing convergence. > > Best regards, > > Kumar.
