[phenixbb] radiation damaged residues occupancy refinement

Mikalai Lapkouski gort105 at gmail.com
Tue Nov 20 06:59:39 PST 2012


Thank you very much!   I was making it indeed incorrect. The one you showed
works just fine.

Thank you,



On Tue, Nov 20, 2012 at 3:54 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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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