Restraints dictionary submitted for approval

Brian H. Toby Brian.Toby at ANL.gov
Wed Jun 30 18:13:55 BST 2010


I have done such refinements. There are occasions where two different rigid bodies may share an atom. One such project for me was neopentane (CH3)4C which I modeled as 4 CH3C groups sharing a single  central C atom. 

Brian

On Jun 29, 2010, at 7:54 PM, James Hester wrote:

> Dear COMCIFS members and observers:
> 
> Herbert's comment and suggested solution make sense to me, but I
> rarely have a need to do such refinements.  Would anybody else like to
> comment on his suggestion?
> 
> James.
> 
> On Tue, Jun 8, 2010 at 10:54 PM, Herbert J. Bernstein
> <yaya at bernstein-plus-sons.com> wrote:
>> Dear Colleagues,
>> 
>> atom_site_rigid_body_id seems intended to allow a given atom
>> to be part of only a single rigid body.  Should we not also
>> allow for the possibility of hinge points in which a single atom
>> may be part of two rigid bodies being joined?  The current
>> definition only allows for two rigid bodies linked by a bond,
>> rather than by a common atom.  If we do this, this will require
>> another category organized by the rigid body id with pointers
>> to the atoms in the body, rather than the current approach of
>> pointers from atom_site to the rigid bodies.
>> 
>> I would suggest an atom_site_rigid_bodies catgeory, with
>> _atom_site_rigid_bodies_id and atom_site_rigid_bodies_label
>> to give the rigid body id and atom site label pairs involved.
>> 
>> Regards,
>>  Herbert
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> =====================================================
>>  Herbert J. Bernstein, Professor of Computer Science
>>   Dowling College, Kramer Science Center, KSC 121
>>        Idle Hour Blvd, Oakdale, NY, 11769
>> 
>>                 +1-631-244-3035
>>                 yaya at dowling.edu
>> =====================================================
>> 
>> On Tue, 8 Jun 2010, James Hester wrote:
>> 
>>> Dear COMCIFS members,
>>> 
>>> Ilia Guzei and David Brown have submitted the dictionary appended below
>>> for approval by COMCIFS.
>>> The dictionary defines items for reporting restraints and constraints
>>> applied during structure
>>> refinement.  They have consulted with the principal writers of refinement
>>> software as well as with
>>> the Core Dictionary Maintenance Group who have approved the attached
>>> document.  The dictionary
>>> contains comments that explain the philosophy behind the dictionary as
>>> well as identifying the
>>> different restraints and constraints that are covered.
>>> 
>>> I suggest that voting members of COMCIFS register their vote to
>>> approve/reject as soon as is
>>> practicable, but in any case no more than 6 weeks from today's date.
>>> 
>>> James Hester
>>> 
>>> 
> 
> 
> 
> 
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Brian H. Toby, Ph.D.                            office: 630-252-5488
Senior Physicist/Section Head for Scientific Software
Advanced Photon Source
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