[phenixbb] phenix.refine change: support for residues on symmetryelements

chern chern at ualberta.ca
Sun Dec 27 14:03:34 PST 2009

when I submitted a pdb with some waters on a twofold sym. axis with 
occupancies =1, the PDB wanted occupancies 0.5.
They do not want to take into account your "taken into account internally".


----- Original Message ----- 
From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>
To: <phenixbb at phenix-online.org>
Sent: Sunday, December 27, 2009 11:24 AM
Subject: [phenixbb] phenix.refine change: support for residues on 

> The current development version of phenix.refine (dev-268 or later)
> supports residues located on symmetry elements, e.g. SO4 on a three-fold
> axis. phenix.refine now computes structure factors slightly differently
> compared to older versions.
> The new rules are:
> - Atoms with occupancy == 1 are subject to automatic handling of the
>  symmetry.
>  Example:
>    An atom near a three-fold axis (distance to symmetry copy <= 0.5 A)
>    is moved onto the axis and constrained in refinement to stay on
>    the axis. The "special position factor" (1/3 is this case) is taken
>    into account internally. The factor does not appear in the occupancy.
> - Atoms with occupancy != 1 are assumed to take the special position
>  factor into account in the occupancy. Automatic handling of the
>  symmetry is turned off.
>  Example:
>    A disordered SO4 molecule near a three-fold axis should have
>    occupancies of 0.33 for all atoms.
> - If all atoms in a residue have occupancies != 1, all
>  nonbonded symmetry interactions between the atoms in the
>  residue are disabled.
> These three rules are meant
>  - to bring phenix.refine in line with other programs and the PDB.
>  - "to do the right thing" in most cases without manual intervention.
> Please let me know if you see problems with the new way phenix.refine
> uses occupancies to determine special position constraints and
> exclusions for nonbonded symmetry interactions.
> Does anyone need atoms with partial occupancies but constrained to
> stay on a symmetry axis during refinement?
> Ralf
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