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RE: Purely calculated structural data in CIF

  • To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group<coredmg@iucr.org>
  • Subject: RE: Purely calculated structural data in CIF
  • From: "Bollinger, John C via coreDMG" <coredmg@iucr.org>
  • Date: Fri, 25 Feb 2022 17:00:03 +0000
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  • Cc: "Bollinger, John C" <John.Bollinger@STJUDE.ORG>
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  • References: <eec82bb2-e0c6-defa-9667-83c64e935af2@iucr.org>

Dear Mike,

 

As far as I am aware, we have no convention for this in Core CIF, but in mmCIF, it appears that one would be expected to use …

 

_exptl.method 'theoretical model'

 

… to flag a computed structure.  Other values of that data name supported by mmCIF provide for identifying various kinds of diffraction and NMR experiments by which the associated structure was determined.  We could consider adding a corresponding item to Core CIF to support such marking going forward, but of course that does not help with recognizing existing CIFs describing computed structures.

 

As for identifying existing core CIFs describing structures determined ab initio or from molecular modeling, I don’t see a better approach than heuristics such as you describe already using.  Additional characteristics that such heuristics might check, especially in the context of checkCIF, would be absence of non-null values for substantially all data names in the _diffrn*, _exptl*, _refine*, _refln* and _reflns* categories.  Exceptions that  might be expected to be present include the proposed _exptl_method item; *_details items; and a handful of items, such as _exptl_crystal_absorpt_coefficient_mu, that are actually computed from the structure rather than being measured.

 

Best regards,

 

John Bollinger

 

 

--

John C. Bollinger, Ph.D., RHCSA

Computing and X-Ray Scientist

Department of Structural Biology

St. Jude Children's Research Hospital

John.Bollinger@StJude.org

(901) 595-3166 [office]

www.stjude.org

 

 

 

 

From: coreDMG <coredmg-bounces@iucr.org> On Behalf Of Mike Hoyland via coreDMG
Sent: Thursday, February 24, 2022 11:03 AM
To: coredmg@iucr.org
Cc: Mike Hoyland <mh@iucr.org>
Subject: Purely calculated structural data in CIF

 

Caution: External Sender. Do not open unless you know the content is safe.

 

Dear All,

We are currently working on improving the checkCIF handling of powder diffraction CIFs, and have coincidentally fallen across an issue with handling purely calculated structural data, e.g. by DFT calculation. So far we have relied on finding the use of "DFT" within various datanames, e.g.

_computing_structure_solution
_diffrn_measurement_device_type

There is no guarantee of course that it would be present in this form.

Therefore, I would like to ask if anyone has any thoughts about how we would be able to simply identify or mark a particular structural datablock as containing calculated rather than experimental data.

With thanks for any thoughts or suggestions,

Mike Hoyland
Systems Developer
IUCr, Chester



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