On Tue, Nov 20, 2012 at 6:41 AM, Mikalai Lapkouski
<gort105@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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