[phenixbb] radiation damaged residues occupancy refinement

Mikalai Lapkouski gort105 at gmail.com
Tue Nov 20 06:41:54 PST 2012

     Right, the problem is that these three atoms form carboxyl group of
Glu, and if I put them (I tried this option) in one occupancy constrained
group, occupancies are  still refined individually with the sum between
three atoms =1. From chemistry point of view I think carboxyl group leaves
as one entity, so occupancy should be the same between all three atoms. Is
there another way how to constrain it between three atoms if it is not the
case of alt conformation?

Thank you

On Tue, Nov 20, 2012 at 2:27 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Tue, Nov 20, 2012 at 3:29 AM, Mikalai Lapkouski <gort105 at gmail.com>wrote:
>> I tried to set the occupancy for those atoms 0.8 and refine individually.
>> But obviously occupancies for those atoms are individually refined to
>> different values which I dont think is the right way. Is there a way of how
>> to refine occupancies for those atoms so that they remain identical after
>> refinement (say all have 0.6)?
> I'm a little surprised that the atoms within a residue aren't already
> constrained to be the same occupancy, but that may only apply if they're
> labeled as an alternate conformer.  But I think all you need to do this is
> to define them as a constrained group, as described here:
> https://www.phenix-online.org/version_docs/dev-1218/refinement.htm#anch111
> (scroll down to Example 4 for the messy details.)  If you're using the
> GUI, you can find the relevant controls by selecting "Occupancy" from the
> menu labeled "Modify atom selections for" below the strategy choices.
> -Nat
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