Draft definition for _diffrn_measurement.specimen_adhesive
James Hester
jamesrhester at gmail.com
Fri Aug 7 03:40:25 BST 2020
There having been no further comments on the most recent definition, I
declare it accepted and will pass it to the technical editor for
incorporation into the next version. Thank you all for your contributions,
keep them coming, there are plenty of draft definitions in the pipeline.
On Mon, 20 Jul 2020 at 12:27, James Hester <jamesrhester at gmail.com> wrote:
> I have redrafted the definition to take into account John B's comments.
> Please feel free to improve the wording.
>
> _description.text
> ;
> The way in which the sample is attached to the sample holder, including
> the type of adhesive material used if relevant.
> The sample holder is usually wholly outside the beam, whereas the
> attachment method may cause non-sample material to be
> illuminated. If the attachment method is not included in the list below,
> 'Other' should be chosen and details provided in
> _diffrn_measurement.specimen_attachment_details.
> ;
> _type.contents Code
> loop_
> _enumerated_set.case
> _enumerated_set.detail
> epoxy "An epoxy glue"
> oil "An oil"
> grease "A type of grease, for example hydrocarbon or silicone
> grease"
> frozen_liquid "A frozen liquid, not water or oil"
> other "A method not listed here"
> ice "The specimen is frozen in place using water ice"
> mechanical "The specimen is held in place by mechanical forces, e.g.
> capillary or pressure cell"
>
> save_
>
> save_diffrn_measurement.specimen_attachment_details
> _definition.id '_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 Thu, 9 Jul 2020 at 00:39, James Hester <jamesrhester at gmail.com> wrote:
>
>> 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_
>>>
>>> ====
>>>
>>> --
>>>
>>> T +61 (02) 9717 9907
>>> F +61 (02) 9717 3145
>>> M +61 (04) 0249 4148
>>>
>>> _______________________________________________
>>> coreDMG mailing list
>>> coreDMG at iucr.org
>>> http://mailman.iucr.org/cgi-bin/mailman/listinfo/coredmg
>>> <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmailman.iucr.org%2Fcgi-bin%2Fmailman%2Flistinfo%2Fcoredmg&data=01%7C01%7Cjohn.bollinger%40stjude.org%7Cac63d4a655bd43cbfc3608d822e38ffa%7C22340fa892264871b677d3b3e377af72%7C0&sdata=A5OlQjYTy7WGgfYKYXDHIUWKHoIMSUJ4ckcN2ZFvnCw%3D&reserved=0>
>>>
>>>
>>>
>>>
>>> --
>>>
>>> "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
>>>
>>>
>>>
>>>
>>> --
>>>
>>> T +61 (02) 9717 9907
>>> F +61 (02) 9717 3145
>>> M +61 (04) 0249 4148
>>>
>>> ------------------------------
>>>
>>> Email Disclaimer: www.stjude.org/emaildisclaimer
>>> Consultation Disclaimer: www.stjude.org/consultationdisclaimer
>>>
>>
>>
>> --
>> T +61 (02) 9717 9907
>> F +61 (02) 9717 3145
>> M +61 (04) 0249 4148
>>
>
>
> --
> T +61 (02) 9717 9907
> F +61 (02) 9717 3145
> M +61 (04) 0249 4148
>
--
T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.iucr.org/pipermail/coredmg/attachments/20200807/2540f4a1/attachment-0001.html>
More information about the coreDMG
mailing list