Draft definition for _diffrn_measurement.specimen_adhesive
James Hester
jamesrhester at gmail.com
Wed Jul 8 15:39:20 BST 2020
So how about we remove 'clay' and 'magnet' and add 'grease' and
'capillary'? If anybody knows of other common methods, please contribute
them.
I think a diamond anvil cell would be more appropriately handled by the
high pressure dictionary when it appears, so the definition should be
written to somehow exclude sample environment apparatus.
On Wed, 8 Jul 2020 at 23:21, Bollinger, John C <John.Bollinger at stjude.org>
wrote:
> With respect to _diffrn_measurement.specimen_attachment_type:
>
>
>
> The description “viscous oil” seems a bit restrictive. I often use a
> low-(room-temperature-)viscosity oil as an adhesive, but that seems to be
> excluded from the “oil” category for no clear reason. On the other hand, I
> sometimes use a silicone or hydrocarbon grease, and it is my impression
> that that is relatively common among chemical crystallographers, yet that
> does not appear to fit in any of the specific options, either.
>
>
>
> Furthermore, I find the appearance of the “clay” and “magnet” options
> surprising and potentially confusing. I am familiar with the use of these
> alternatives and others for affixing a pin to a goniometer head, but I
> think this item is about the means of attaching specimen to holder, not
> about the means of attaching different components of the holder to each
> other. Do people really use clay and / or magnets for affixing specimens?
> If those are alternatives we indeed want to designate explicitly, then
> perhaps it would be useful for the item description to clarify what “the
> sample” is enough to distinguish between different uses of clay / magnets.
> Perhaps a useful distinguishing characteristic would be that an attachment
> device or material will typically be exposed to the primary beam during the
> ordinary course of the experiment, though of course that is not a complete
> characterization.
>
>
>
> Also, should there be an explicit option covering diamond anvil cells and
> similar devices? Perhaps ‘mechanical’? I guess capillaries might fit in
> such a category, too.
>
>
>
>
>
> 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 [mailto:coredmg-bounces at iucr.org] *On Behalf Of *James
> Hester via coreDMG
> *Sent:* Tuesday, July 07, 2020 9:06 PM
> *To:* Distribution list of the IUCr COMCIFS Core Dictionary Maintenance
> Group <coredmg at iucr.org>
> *Cc:* James Hester <jamesrhester at gmail.com>
> *Subject:* Re: Draft definition for _diffrn_measurement.specimen_adhesive
>
>
>
> *Caution: External Sender*
>
>
>
> Here is an updated definition for the specimen attachment data names,
> taking into account comments from here and at Github. Further comments
> welcome, if none are forthcoming I will add these definitions to the core
> dictionary.
>
>
>
> save_diffrn_measurement.specimen_attachment_type
> _definition.id
> <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdefinition.id%2F&data=01%7C01%7Cjohn.bollinger%40stjude.org%7Cac63d4a655bd43cbfc3608d822e38ffa%7C22340fa892264871b677d3b3e377af72%7C0&sdata=gBYxYarE8zNwDofGxq0w1FbVuhh1cT6F%2B%2Fg5FpL9PBA%3D&reserved=0>
> '_diffrn_measurement.specimen_attachment_type'
> _description.text
> ;
> The way in which the sample is attached to the sample holder, including
> the type of adhesive material used if relevant. If
> the attachment method is not included in the list below, 'Other' should be
> chosen and details provided in
> _diffrn_measurement.specimen_attachment_special_details.
> ;
> _type.contents Code
> loop_
> _enumerated_set.case
> _enumerated_set.detail
> epoxy "An epoxy glue"
> oil "A viscous oil"
> frozen_liquid "A frozen liquid, not water or oil"
> magnet "Sample is held in place by magnetic field"
> clay "Modelling clay"
> other "A method not listed here"
> ice "The specimen is frozen in place using water ice"
>
> save_
>
> save_diffrn_measurement.specimen_attachment_details
> _definition.id
> <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdefinition.id%2F&data=01%7C01%7Cjohn.bollinger%40stjude.org%7Cac63d4a655bd43cbfc3608d822e38ffa%7C22340fa892264871b677d3b3e377af72%7C0&sdata=gBYxYarE8zNwDofGxq0w1FbVuhh1cT6F%2B%2Fg5FpL9PBA%3D&reserved=0>
> '_diffrn_measurement.specimen_attachment_details'
> _description.text
> ;
> A description of the method of attachment of the sample to the sample
> holder. The general method of attachment
> should be described using _diffrn_measurement.specimen_attachment_type
> ;
> loop_
> _description_example.case
> "UHU Super Glue ultrafast gel"
> "Fluorinert"
> "Plasticine"
> "Sample was held tightly by a custom aluminium wire framework attached to
> the sample holder"
>
> save_
>
>
>
>
>
>
>
> On Tue, 23 Jun 2020 at 22:36, Peter Murray-Rust <pm286 at cam.ac.uk> wrote:
>
> Possible typo?
> https://en.wikipedia.org/wiki/Fluorinert
> <https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FFluorinert&data=01%7C01%7Cjohn.bollinger%40stjude.org%7Cac63d4a655bd43cbfc3608d822e38ffa%7C22340fa892264871b677d3b3e377af72%7C0&sdata=ZYg8WmKpO65CnkxnjTc1B5eQzo%2BaoyU0tK4Gmcn%2BFuM%3D&reserved=0>
>
>
>
> On Tue, Jun 23, 2020 at 7:10 AM James Hester via coreDMG <coredmg at iucr.org>
> wrote:
>
> Dear Core DMG,
>
>
>
> Please see the following proposed new definition for describing the
> adhesive used to attach a single crystal specimen to a capillary or other
> sample holder attached to a goniometer head. I have provided one definition
> that selects from an enumerated list, useful for machine processing, and
> another that allows free-form text so that brand names and other details
> can be included. If you know of any methods of adhesion that are not
> covered in the following list, please contribute them, and if I have
> suggested anything that is not used in practice, please let me know.
>
>
>
> ====
>
> save_diffrn_measurement.specimen_adhesive_type
>
> _definition.id
> <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdefinition.id%2F&data=01%7C01%7Cjohn.bollinger%40stjude.org%7Cac63d4a655bd43cbfc3608d822e38ffa%7C22340fa892264871b677d3b3e377af72%7C0&sdata=gBYxYarE8zNwDofGxq0w1FbVuhh1cT6F%2B%2Fg5FpL9PBA%3D&reserved=0>
> '_diffrn_measurement.specimen_adhesive_type'
>
> _description.text
>
> ;
>
> The type of the adhesive material used to attach the sample to a sample
> holder.
>
> ;
>
> loop_
>
> _enumerated_set.case
>
> _enumerated_set.detail
>
> Epoxy "An epoxy glue"
>
> Oil "A viscous oil"
>
> Frozen_Liquid "A frozen liquid, not water or oil"
>
> Magnet "Sample is held in place by magnetic field"
>
> Clay "Modelling clay"
>
> . "No adhesive used"
>
> Ice "The specimen is frozen in place using water ice"
>
>
>
> save_
>
>
>
> save_diffrn_measurement.specimen_adhesive_details
> _definition.id
> <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdefinition.id%2F&data=01%7C01%7Cjohn.bollinger%40stjude.org%7Cac63d4a655bd43cbfc3608d822e38ffa%7C22340fa892264871b677d3b3e377af72%7C0&sdata=gBYxYarE8zNwDofGxq0w1FbVuhh1cT6F%2B%2Fg5FpL9PBA%3D&reserved=0>
> '_diffrn_measurement.specimen_adhesive_details'
> _description.text
> ;
> A description of the method of attachment of the sample to the sample
> holder. The general method of attachment
>
> should be described using _diffrn_measurement.specimen_adhesive_type
> ;
> loop_
> _description_example.case
> "UHU Super Glue ultrafast gel"
>
> "Flourinert"
>
> "Plasticine"
>
> "Sample was held tightly by a custom aluminium wire framework attached to
> the sample holder"
>
>
>
> save_
>
> ====
>
> --
>
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> M +61 (04) 0249 4148
>
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>
>
> --
>
> "I always retain copyright in my papers, and nothing in any contract I
> sign with any publisher will override that fact. You should do the same".
>
>
>
> Peter Murray-Rust
> Reader Emeritus in Molecular Informatics
> Unilever Centre, Dept. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069
>
>
>
>
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>
> T +61 (02) 9717 9907
> F +61 (02) 9717 3145
> M +61 (04) 0249 4148
>
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