Using _atom_site_disorder_* data names to describe compositional disorder?

[James H]

We can update the relevant section of the core CIF Vol G chapter and the
core CIF dictionary if there are no objections forthcoming from the rest of
the DMG.

On Thu, 11 Nov 2021 at 05:18, Herbert J. Bernstein <yayahjb at gmail.com>
wrote:

> This overlaps strongly with the presentation of microheterogenity in
> mmCIF, and "variant" in imgCIF.  We
> should try to work out a reasonably consistent approach, if possible, or
> at least document the overall subject.  -- Herbert
>
> On Wed, Nov 10, 2021 at 12:34 PM Bollinger, John C via coreDMG <
> coredmg at iucr.org> wrote:
>
>>
>>
>> I not only have no objection, I think it is essential to make that
>> allowance to accommodate a large body of traditional practice.  Popular
>> crystallographic refinement programs that emit CIF (SHELXL, for example) do
>> not provide distinct mechanisms for modelling these different varieties of
>> disorder, and they do emit CIF using the _atom_site_disorder_* data names
>> to describe the results.
>>
>>
>>
>> Moreover, I’m not convinced that there is a clean distinction between
>> these disorder types.  For example, when there is a compositional disorder
>> involving elements with significantly different size or different charge,
>> it is not so unusual for that to be correlated with changes in the
>> positions of the neighboring atoms, which are sometimes resolvable.
>>
>>
>>
>>
>>
>> Regards,
>>
>>
>>
>> John
>>
>>
>>
>> --
>>
>> John C. Bollinger, Ph.D., RHCSA
>>
>> Computing and X-Ray Scientist
>>
>> Department of Structural Biology
>>
>> St. Jude Children's Research Hospital
>>
>> John.Bollinger at StJude.org
>>
>> (901) 595-3166 [office]
>>
>> www.stjude.org
>>
>>
>>
>>
>>
>>
>>
>> *From:* coreDMG <coredmg-bounces at iucr.org> *On Behalf Of *James H via
>> coreDMG
>> *Sent:* Tuesday, November 9, 2021 6:58 PM
>> *To:* Distribution list of the IUCr COMCIFS Core Dictionary Maintenance
>> Group <coredmg at iucr.org>
>> *Cc:* James H <jamesrhester at gmail.com>
>> *Subject:* Using _atom_site_disorder_* data names to describe
>> compositional disorder?
>>
>>
>>
>> *Caution: External Sender. Do not open unless you know the content is
>> safe.*
>>
>>
>>
>> Dear Core DMG,
>>
>>
>>
>> It has been noticed [1] that the _atom_site_disorder_* data names, which
>> are designed to describe positional disorder of a group of bonded atoms,
>> could also be used to describe compositional disorder, where one site is
>> randomly occupied by one of two (or more) atom types. Vol G First edition
>> describes two other methods for recording compositional disorder, and only
>> talks of positional disorder of a group of atoms when discussing the
>> _atom_site_disorder_* data names. It seems clear that these data names were
>> designed with groups of atoms in mind, but nothing seems to explicitly
>> exclude using them for compositional disorder.
>>
>>
>>
>> The question for you all is, are there any objections or problems any of
>> you can see with explicitly allowing compositional disorder to be described
>> using _atom_site_disorder_* data names?
>>
>>
>>
>> thanks,
>>
>> James.
>>
>>
>>
>> [1] https://github.com/COMCIFS/cif_core/issues/251
>> <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCOMCIFS%2Fcif_core%2Fissues%2F251&data=04%7C01%7Cjohn.bollinger%40stjude.org%7C7e27ca7786ac4fe19b3508d9a3e520d2%7C22340fa892264871b677d3b3e377af72%7C0%7C0%7C637721027531165379%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=MEFiJzK3yjU1mzbneav5LO4HN69ObDbT80QfklCRI9Q%3D&reserved=0>
>> --
>>
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>> M +61 (04) 0249 4148
>>
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