Hi,

Thanks for your advice. It’s still not working. I use the phenix gui version and if I set, for example,

chain A and resid 249
chain A and resid 252
chain S and resid 1702

as a constrained group at the occupancy refinement selections (the two residues have 2 conformations both and the water is there just if the conformation of residue 252 is B) the refinement just makes the residues a constrained group alone making even their main chain occ. something like 0.49 as for the both of the side chains too. And it also kicks them a bit out of their densities. So how to continue? What am I doing wrong?

Best regards,
Helena

Folmer Fredslund <[email protected]> kirjoitti 11.1.2016 kello 15.20:

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 <[email protected]>:

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" <[email protected]> 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