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. -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319
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.
Hi Pavel, My resolution is 2.1 Ang.. So its high enough for individual B-Factor refinement. The density for this particular atom is not that good, which explains the high B-Factor for this. As the other atoms of the ligand have reasonble B-Factors compared to the main chain they seems to be nearly fully occupied. I am a bit in doubt about the possibilty that between the two connected atoms the B-Factor changes so drastically. The R-Factors are absolutely O.K R/Rfree 20,32/25,03 rms bond 0,007 rms angle 1,363. I thought already one could maybe allow a bit more deviation for bond and angles. Christian Am Mittwoch 27 Oktober 2010 18:45:42 schrieb Pavel Afonine:
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.
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Hi Christian,
My resolution is 2.1 Ang.. So its high enough for individual B-Factor refinement. The density for this particular atom is not that good, which explains the high B-Factor for this. As the other atoms of the ligand have reasonble B-Factors compared to the main chain they seems to be nearly fully occupied. I am a bit in doubt about the possibilty that between the two connected atoms the B-Factor changes so drastically. The R-Factors are absolutely O.K R/Rfree 20,32/25,03 rms bond 0,007 rms angle 1,363. I thought already one could maybe allow a bit more deviation for bond and angles.
well in this case it's hard to tell anything without looking at the files. What's happening shouldn't normally happen (based on what you explain) and if it happens then there must be a reason. If you want you can send me the files (model+data, and indicated the problem atoms) (OFF-LIST) and I will have a look. Pavel.
participants (2)
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Christian Roth -
Pavel Afonine