[phenixbb] Support for residues on symmetry elements - first reaction

[Peter Zwart]

==  : equal

!= : not equal

2009/12/27 Felix Frolow <mbfrolow at post.tau.ac.il>:
> 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: mbfrolow at post.tau.ac.il
> 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
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>
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-- 
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
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