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Re: Restraints dictionary submitted for approval

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@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@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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