Using _atom_site_disorder_* data names to describe compositional disorder?

[Herbert J. Bernstein]

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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