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

Jeff Headd jjheadd at lbl.gov
Fri Oct 26 13:37:55 PDT 2012

That is definitely some strange behavior going on there. The position of
the N-H atom is in part determined by the position of carbonyl carbon in
the preceding residue, but usually it would have the matching altID
associated with it. In the example you've sent, it looks like Reduce may
not be adding this hydrogen correctly.

Would you be willing to send me your entire PDB file directly (NOT to the
list) so that I could see why Reduce is behaving that way?

I'm not sure about the occupancy problem, though. That should only happen
if there were multiple positions for that hydrogen.


On Fri, Oct 26, 2012 at 4:07 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi,
> 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.
> Pavel
> On 10/26/12 11:39 AM, Nathaniel Echols 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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