[phenixbb] pdb LINK record lost after phenix refine in GUI
pafonine at lbl.gov
Thu Jul 16 22:03:07 PDT 2015
> The serine contains no H atoms and the ligand has H atoms in the
> PDB file. How do Phenix refine deal with this two kind of H atoms at
> nearly the same place?
phenix.refine is a refinement program, not model building. It will
attempt to refine whatever you give it, good or garbage, and, in case of
garbage in, expect garbage out, typically.
So if you have that H that given the new bond should go, then you should
delete it. Perhaps we should detect such cases automatically and deal
with them seamlessly (thoughts, Nigel?) but at present it appears to me
as the next level of sophistication that we haven't gotten to yet.
> I have deleted the H atoms of the ligand, and refined again. The
> coordinate is reasonable without H atoms being seen.
> So, I think the simplest way is to delete all H atom in such resolution.
Yes, this is true.
> Best wishes!
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