Items for the coreCIF dictionary relating to restraints

[David Brown]

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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