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RE: Draft definition for _diffrn_measurement.specimen_adhesive

  • To: "james.r.hester@gmail.com" <james.r.hester@gmail.com>, "Distribution listof the IUCr COMCIFS Core Dictionary Maintenance Group" <coredmg@iucr.org>
  • Subject: RE: Draft definition for _diffrn_measurement.specimen_adhesive
  • From: "Bollinger, John C via coreDMG" <coredmg@iucr.org>
  • Date: Wed, 8 Jul 2020 13:21:08 +0000
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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@StJude.org

(901) 595-3166 [office]

www.stjude.org

 

 

 

 

 

From: coreDMG [mailto:coredmg-bounces@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@iucr.org>
Cc: James Hester <jamesrhester@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     '_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     '_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@cam.ac.uk> wrote:

 

On Tue, Jun 23, 2020 at 7:10 AM James Hester via coreDMG <coredmg@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     '_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     '_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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--

"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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F +61 (02) 9717 3145
M +61 (04) 0249 4148



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