[phenixbb] radiation damaged residues occupancy refinement

[Nathaniel Echols]

On Tue, Nov 20, 2012 at 6:41 AM, Mikalai Lapkouski <gort105 at gmail.com>wrote:

>      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?
>

I suspect you're specifying the selections incorrectly - each constrained
group should have a single selection which includes all atoms in a group
that you want to keep together, and not multiple selections (one per atom).
 If you're using parameter files, this means doing this:

refinement.refine.occupancies {
  constrained_group {
    selection = chain A and resseq 40 and (name CD or name OE1 or name OE2)
  }
}

and not:

refinement.refine.occupancies {
  constrained_group {
    selection = chain A and resseq 40 and name CD1
    selection = chain A and resseq 40 and name OE1
    selection = chain A and resseq 40 and name OE2
  }
}

I tried the first version here and it appears to work as expected.

-Nat
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