[phenixbb] "H" atom refining occupancy with previous altconf residue in sequence

Pavel Afonine pafonine at lbl.gov
Fri Oct 26 14:41:41 PDT 2012

The current behavior is intended one and asserted by regression test:


If you remove hydrogens from that PDB file, and then add them back, 
Reduce will add H on MET30, and its occupancy will be inherited from 
atoms in MET29 that define its position.

phenix.refine in turn will pick up that for occupancy refinement 
according it its default behavior.

Jeff: the occupancy of H in MET30 does match the occupancy of relevant 
atoms in preceding residue (MET29). I verified this with this specific 
example, and also this is asserted in the above test.

We discussed this multiple times in the past and current behavior is the 
consensus one. If this is not what we want then we need to fix Reduce.


On 10/26/12 1:17 PM, Nathaniel Echols wrote:
> On Fri, Oct 26, 2012 at 1:07 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
>> I did not look closely yet but my understanding is that its position is
>> dictated by the next to it residue that has non-blank altlocs, and therefore
>> this hydrogen inherits the conformers. So this behavior is expected. I hoped
>> Jeff will comment on this as he was the first who explained it to me.
> This explains the behavior of phenix.ready_set, but not the change to
> occupancy made by phenix.refine.
> -Nat
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