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Re: Draft CIF dictionary for rgid body description

Dear George,

   I am the guilty party who raised the question of describing a
the common atom case.

   The question for a dictionary is not whether the case is encountered
very often, but whether there is any need for it at all.  The common atom
case is not likely to encountered often, but, as you note, it is does 
happen in special cases.  Having the ability to handle this case in the 
dictionary takes nothing away from the ability to handle
the more frequently encountered rigid-body cases.  Having the ability
to describe this case does not imply that any particular software
package need handle it.  However, it would seem to be 
desirable to be able to describe the common atom case in the dictionary,
so that when the need does arise, we will have some clear, agreed 
terminology to use.

  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769


On Wed, 11 Aug 2010, George M. Sheldrick wrote:

> There is a very good reason why shelxl does not allow an atom to be in
> more than one rigid group: it is mathematically impossible except for the
> special case where the the 'pivot atom' is itself in another rigid group
> which defines its x, y and z coordinates. This special case is very
> complex to program. Restraints are much simpler to implement and probably
> more effective because they distribute the errors more flexibly.
> George
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-3021 or -3068
> Fax. +49-551-39-22582
> On Wed, 11 Aug 2010, David Brown wrote:
>> Dear Colleagues,
>> In January I circulated to you, the coreCIF Dictionary Maintenance Group, the
>> draft of a CIF dictionary containing items for reporting the restraints and
>> constraints that were applied during the final round of refinement.  This was
>> approved by this group after a six week consultaion period and passed on to
>> COMCIFS for final approval.  During this stage an objection was raised that
>> under the proposal it was not possible for an atom to belong to more than one
>> rigid body, because the rigid bodies were defined by a flag in the atom_site
>> list which identified which rigid body a partcular atom belonged to.
>> In order to address this weakness, Ilia Guzei and I have proposed an amendment
>> to the earlier draft.  This is more flexible in that it defines each rigid
>> body in terms of any atom in the atom_site list together with a symmetry
>> operation.  This places no restriction on the number of rigid bodies an atom
>> can belong to.  I am circulating this amendment in the attached ASCII file
>> which contains the amended dictionary text.
>> Can you please check this and respond to this Discussion List with your
>> approval or reservation before September 10 (2010-09-10).  If there are no
>> unresolved issues at that time, I will incorporate this amendment into the
>> original restraint dictionary and pass it back to COMCIFS for final approval.
>> I am looking forward to heariing from you
>> David Brown
>> Chair CoreCIF DMG
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