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

Pavel Afonine pafonine at lbl.gov
Tue Oct 30 14:04:05 PDT 2012

Hi Alex,

it's a result of inconsistent behavior of phenix.reduce and 
phenix.ready_set (as Nat me pointed out), and so I overlooked this 
caveat in handling in phenix.refine. This will be fixed some time in the 


On 10/30/12 1:57 PM, Alexander Scouras wrote:
> Sorry for not getting back to you sooner.
> I'm working at better than 1.0A resolution for some structures, so am able to determine histidine protonation state in some cases. So yes, I turned off the automatic hydrogen additions. Now that I understand the behavior, I can work with it.  Clearing up the histidines can wait until the end of refinement, after I've worked out the altconfs anyway.
> Jeff: If you still want my refinement history, I can send it along, but it sounds like (according to Pavel) this is the expected behavior and I just need to change my refinement routine a little bit.
> On Oct 26, 2012, at 1:20 PM, Nathaniel Echols <nechols at lbl.gov> wrote:
>> On Fri, Oct 26, 2012 at 1:06 PM, Alexander Scouras <scouras at berkeley.edu> wrote:
>>> I was wondering if something like that was the idea, though I guess I might have expected the main chain nitrogen to also get an alternate conformation. Hydrogens are just second class atoms I guess, and that dihedral would be more important than actually moving the N.
>>> When running iterative refinement between Phenix and Coot, adding altconfs as they come up, should you regularly be running ready_set (or anything else) after?  I always just save the coordinates and then load that pdb in the next round of phenix.refine.
>> I would continually run phenix.ready_set in this case - actually, if
>> you're using the phenix.refine GUI I think you can just click
>> "Automatically add hydrogens to model" and everything else will be
>> done automatically.  (If not, that's a bug too!)  Unless you are
>> performing neutron refinement or some very specialized high-resolution
>> enzymology, it is unlikely that you will actually care about
>> preserving the hydrogen positions from round to round anyway.
>> -Nat
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