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

Alexander Scouras scouras at berkeley.edu
Tue Oct 30 13:57:47 PDT 2012

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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