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

Alexander Scouras scouras at berkeley.edu
Fri Oct 26 13:06:43 PDT 2012

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.  

It looks like my previous refinements of these structures were using the 1.7 branch, so it could have been introduced in 1.8.0 indeed.

Running phenix.ready_set did not initially correct the hydrogens, probably because it didn't know what to do with hydrogens in partial occupancies. It worked fine after I removed all hydrogens from the structure though.

On Oct 26, 2012, at 11:39 AM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Thu, Oct 25, 2012 at 8:05 PM, Alexander Scouras <scouras at berkeley.edu> wrote:
>> After a series of residues (1+) with alternate conformations, the H atom of the next residue seems to lock its occupancy to that of the final conformation of the previous residue.  Hence I'm getting several H's with 0.1-0.5 occupancy on single conformation residues, where the entire rest of the residue has occupancy 1.  This happens after every altconf series, and showed up in two separate structures I've worked on this week.
>> Within a series of 2+ residues with altconfs, the H's refine correctly with their altconf groups.  So it isn't just that all subsequent residue's H's are getting overridden.
>> This behavior seems to have started with 1.8.1-1168, or at least previous refinements of the same structure didn't do this.  64 bit build on Retina MBP running OS X 10.8.2.
>> I couldn't google any reference to this behavior, so assuming it's a new bug I can send along source files.
> Very interesting - this is also reproducible with a simple test case
> and the latest code.  Judging from the revision history, it looks like
> this probably would have happened with version 1.8 too.  I am not
> entirely sure what the code is doing, but I think it is partly based
> on the assumption that if you have an alternate conformation for the C
> and/or CA atoms of a residue, the H atom for the next residue will
> also have alternate conformations.  This is in fact what
> phenix.ready_set will do - if you re-run it on your input PDB file,
> you will have A/B/C conformations for Met30 H.  So I'm inclined to
> suggest simply doing this (it is the most chemically sensible
> approach), but the behavior of phenix.refine when no alternate
> conformer is present for H does appear to be a bug.
> -Nat
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