Ralf ----- GREAT However I do not get what it is ==1 and !=1 Are they have meaning or it is encoding striking back? And to the last question: yes, it is good to keep coordinates constrained to stay on the symmetry element. It should be a default. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: [email protected] Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Dec 27, 2009, at 20:24 , Ralf W. Grosse-Kunstleve wrote:
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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb