[phenixbb] pdb LINK record lost after phenix refine in GUI

Pavel Afonine pafonine at lbl.gov
Thu Jul 16 22:03:07 PDT 2015

Hi Lu,

>     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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