Using _atom_site_disorder_* data names to describe compositional disorder?

[James H]

Dear Core DMG,

There having been no objections to the use of _atom_site_disorder_* to
describe compositional disorder, I will set the wheels in motion to update
the Volume G chapter and dictionary.

Thank you for your input.

James.

On Fri, 12 Nov 2021 at 14:43, James H <jamesrhester at gmail.com> wrote:

> 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>
>>> --
>>>
>>> T +61 (02) 9717 9907
>>> F +61 (02) 9717 3145
>>> M +61 (04) 0249 4148
>>>
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>>
>
> --
> T +61 (02) 9717 9907
> F +61 (02) 9717 3145
> M +61 (04) 0249 4148
>


-- 
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