Zero or low B-factor in pdb file

Model Building
1

Hi all,

I am seeking advice regarding B-factors in a PDB file. I have completed model building, but when I open the PDB file, I notice that many atoms have either zero or unusually low B-factors which I believe should not be the case. I tried running real-space refinement in phenix after replacing zero B-factors with random values, but it didn’t work. I would appreciate any insights or suggestions on how to address this.

Thanks in advance

2

Hi Wynn,

We are having the same issues here with Phenix refinement - did you get any help with this?
Perhaps I should be over on the phenix bb; we’ve tried Phenix v 1.20.1-4487 and 1.21.2-5419, both giving B-factor 0 for e.g. side chain Carbons and Calphas in good density.

Hope we can find a fix!