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Re: Items for the coreCIF dictionary relating to restraints



Title:
Dear George,

Thanks for your email and the useful suggestions it contains.  Although I had thought our proposal was already complete, we will have another look at it in the light of your comments and others we have received, keeping in mind also that SHELX is the mostly widely used program.

I can appreciate from first hand experience that one's interests change with the years and what looked like an exciting challenge at one stage in life becomes a burden in another.  However, SHELX is so widely used that I cannot imagine that someone will not step in to keep it up to date.  I am not too worried if our CIF restraint items are not incorporated right away; the fact that they exist will mean that they are available when someone wants to use them.

As you point out there are still challenges out there and I wish you well with them.  I am writing a review for Chemical Reviews and have had fun rereading your interesting paper on identifying metal atoms in protein structures.

Thanks again for your comments.

David



George M. Sheldrick wrote:
Dear David,

The proposed list looks very sensible to me and Ilia has done an excellent 
job of sorting it out. I like the idea of using an esd of zero to 
distinguish constraints from restraints.

I may be mistaken, but as far as I can see, the probably most commonly 
applied constraint in SHELXL (and probably other programs too) is still 
not covered. I refer to the case where there are disordered solvent 
molecules or side-chains, where one GROUP of atoms (e.g. a solvent 
molecule) have the same refinable occupancy p and the atoms in the 
alternative groupall have occupancies 1-p. This is a powerful constraint 
because only one extra parameter p can describe the occupancies of a 
large number of atoms. Maybe there is a way of using 'restraint 10' for 
this but it is not clear to me, and such a common case should be covered 
explicitely. 

Without a concept that maps onto the SHELX 'free variables' it will 
never be possible to produce a CIF file that enables a refinement to be 
repeated. In my personal opinion this is the primary reason for wanting
to encode the restraints and constraints in CIF, without this it is a 
rather academic exercise.

I am getting old and senile and in addition to plenty of teaching and 
administration have a long list of more exciting things to program - 
primarily in macromolecular crystallography - almost certainly more 
than I will ever manage to achieve - so I have no plans to adapt 
SHELXL to produce these CIF items, even if as seems likely I release
further updates of this program. I have not forgotten what a torture 
it was to create and read CIFs before proper tools were available, 
but it probably made the difference in getting CIF generally accepted
by small molecule crystallographers. Maybe someone else will have 
time to produce software that reads a SHELXL .res file and writes the 
restraints and constraints to a CIF file. 

Best wishes, 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. +49-551-39-2582


On Thu, 13 Dec 2007, David Brown wrote:

Dear Colleagues,

Ilia Guzei and I have put together the attached document describing a way in
which constraints and restraints applied during a structure refinement could
be recorded in a CIF.  There has been some demand for such an addition to the
core dictionary.

I would appreciate it if you could look over the attanched document and let me
have any comments before Jan 20.  The proposal is in the form of CIF examples
as this should be easier to read and understand than reading dictionary code.
We will construct the dictionary code after we have your comments.  You will
have a chance to check the code before the dictionary is submitted for final
COMCIFS approval.

PLEASE MAY I HAVE YOUR COMMENTS BEFORE 20 JANUARY 2008.  Let me know if you
need an extension.

I look forward to hearing from you.

David


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n:Brown;I.David
org:McMaster University;Brockhouse Institute for Materials Research
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email;internet:idbrown@mcmaster.ca
title:Professor Emeritus
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tel;fax:+905 521 2773
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