Hi Christian, what is the resolution? You may want to tighten up the B-factor refinement restraints manually, by making wxu_scale parameter smaller (try several values until the refined B-factors "make sense" and the R-factors are still ok). Alternatively, you may try group B-factor refinement (again, if the resolution is low enough to make individual B-factor refinement not favorable). Also, the high B-factors may simply reflect the fact that those atoms do not have a good density. In this case making the B-factors of bad atoms to be similar to the B-factors of good atoms (by tightening the restraints) is not a good idea. So, as you can see there is a number of nuances that you need to consider. Pavel. On 10/27/10 11:26 AM, Christian Roth wrote:
Dear all,
I did a refinement run with a built in ligand. Within the ligand the B-factor jumps between two connected atoms from 60 up ~110, which is i think a bit too much. Is there a way to restrain the B-factors that they could not jump so much. I would accept negative difference density for the atom. Maybe the ligand is a bit degraded.
Best regards
Christian
@Pavel Tanks for your suggestions with occupancy refinement and B-factors.