# [phenixbb] occupancy group definition

Christian Roth christian.roth at bbz.uni-leipzig.de
Tue Jun 26 10:38:23 PDT 2012

```Hi  Pavel

thanks for pointing that out and the small lecture about Boolean Algebra. It
is sometimes a bit tricky for me.

Best Regards

Christian

Am Montag 25 Juni 2012 22:32:14 schrieb Pavel Afonine:
> Hi Christian,
>
> if you don't specify any selections for occupancy refinement manually it
> will be done automatically just right.
>
> If you still want to do it manually, then the correct selection would be
> (which is equivalently to what phenix.refine does automatically in this
> case)
>
> refinement {
>    refine {
>      occupancies {
>        constrained_group {
>          selection = chain A and resseq 130 and altloc A
>          selection = (chain A and resname PMS and altloc B) or (chain A
> and resseq 130 and altloc B)
>        }
>      }
>    }
> }
>
> In plain English the above selections translate as:
>
> - there will be one refinable occupancy for alternative conformer A of
> residue 130 in chain A; AND
> - there will be one refinable occupancy for alternative conformer B of
> residue 130 in chain A, and residue PMS (*);
> - the sum of the two refinable occupancies above will add up to 1.
>
> (*) Since it is unique (there is no other instances of PMS in your PDB
> file), there is no need to specify chain id and altloc for it, so this
> would work too:
>
> refinement {
>    refine {
>      occupancies {
>        constrained_group {
>          selection = chain A and resseq 130 and altloc A
>          selection = resname PMS or (chain A and resseq 130 and altloc B)
>        }
>      }
>    }
> }
>
> Let me know if you have any questions or need more help with this!
>
> Pavel
>
> On 6/22/12 7:06 AM, Christian Roth wrote:
> > Dear All,
> > I have tried an occupancy refinement for a partially modifed residue.
> > I have split the residue in altloc A and B and the modification (PMSF) is
> > attached on B. I included the PMS moiety as part of the residue and gave
> > them altloc B. I created the cif link. The refinement resulted in a
> > strange mixture of occupancys for PMS  around 0.8 and both Serins 0.23 an
> > 0.77. So PMS is not part of the residue. I am not sure about the correct
> > syntax for the constrained group. At the moment I  have used
> > constrained_group {
> >          selection = chain A and resseq 130 and altloc A
> >          selection = chain A and resname PMS and altloc B
> >        }
> > However the Serine pat of altloc B refines to a value not compatible to
> > the PMS values or the Altloc A value of the serine. How do I incorporate
> > the altloc B for the serine?
> >
> >
> > Christian
> >
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
>

```