[phenixbb] Additional conformations and partially occupied waters

[Folmer Fredslund]

Hi Helena,

I believer this is the relevant bit from the manual:
https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement
(in the examples)


   1.

   Complex occupancy refinement strategy (combination of various available
   occupancy refinement types):

   % phenix.refine data.hkl model.pdb strategy=occupancies occ.params


The amount of atom selections makes it inconvenient to type them all from
the command line. This is why the parameter file occ.params is used and it
contains following lines:

refinement {
  refine {
    occupancies {
      individual = element BR or water
      individual = element Zn
      constrained_group {
        selection = chain A and resseq 1
      }
      constrained_group {
        selection = chain A and resseq 2
        selection = chain A and resseq 3
      }
      constrained_group {
        selection = chain X and resname MAN
        selection = chain X and resseq 42
        selection = chain X and resseq 121
      }
      remove_selection = chain B and resseq 1 and name O
      remove_selection = chain B and resseq 3 and name O
    }
  }
}



Hope this helps,
Folmer

2016-01-11 13:14 GMT+01:00 Christian Roth <christianroth034 at gmail.com>:

> Hi Helena,
> Indeed you have to group the relevant aa and the respective water together
> in a constrained group to avoid your problem and get the occupancies add up
> to 1. This us described in the manual under occupancy refinement. I can't
> access the manual at the moment to give you a more detailed answer.
>
> Cheers
>
> Christian
> On 11 Jan 2016 11:56, "Helena Taberman" <helena.taberman at uef.fi> wrote:
>
>> Hi,
>>
>> I’m trying to refine a structure determined to 1.6 Å resolution. There’s
>> several residues with additional conformations and waters with partial
>> occupancies stating that they would be there when the conformation of the
>> residues allows it. When I try to refine these conformations and partially
>> occupied waters together the refinement kicks the second conformations and
>> water molecules out of their densities, since they are obviously too close
>> to the other additional conformations of the residues or the following
>> residues. What could I do? Should I somehow group them together or what?
>>
>> Best regards,
>> Helena
>>
>> Helena Taberman, Ph.D.
>>
>> University of Eastern Finland
>> Department of Chemistry
>> Joensuu Campus
>> P.O. Box 111
>> FI-80101 Joensuu, FINLAND
>>
>> Mobile: +358 50 337 2488
>>
>>
>>
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-- 
Folmer Fredslund
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