Re: New items relevant to radiation damage

I think that the flux density should also go in the diffrn category. The situation is quite different for x-ray/neutron and electron diffraction. In electron diffraction, the flux density can be (and is) changed easily and frequently, e.g. to match the beam size to the crystal, so it is associated more with the individual experiments than with the radiation setup. For x-ray or neutron diffraction, _diffrn_radiation.peak_flux_density might have some relevance, but for electron diffraction I don't see it - the electron beam can be well focused to (almost) a point, increasing the flux density to very high values, but such a maximum achievable flux density is of little to no relevance to the actual diffraction experiment.

Best regards

Lukas

On 2024-12-12 03:17, James H wrote:

Did the discussion consider which was the most appropriate category for these definitions? I agree that total dose and total exposure time should go in diffrn, as diffrn describes a single measurement with a single specimen so these quantities are well-defined. However, I would normally consider flux density a property of the radiation, so more properly in diffrn_radiation. However, if the flux density is considered to be setup-specific, that is, different specimens would experience a different flux density (that could be determined) due to being at different positions within the beam, then I agree with putting a definition in diffrn. If both scenarios are reasonable, then a fourth definition could be added to diffrn_radiation, something like '_diffrn_radiation.peak_flux_density'

On Sat, 7 Dec 2024 at 00:45, Brian McMahon via coreDMG <coredmg@mailman.iucr.org> wrote:

I have been working with the NanED project on new CIF data names
relevant to electron diffraction, and the suggestion has arisen for a
number of items that allow some assessment of the amount of radiation
that the crystal is subjected to. It seems to me that these terms have
more general application, and so I am posting these suggested
definitions as possible general terms to add to the core dictionary.
Your comments are welcome.

Note that the units of flux density are dependent on the radiation
probe. Note also that the terminology regarding amount of radiation is
often confused and confusing. For example, the mmCIF dictionary has a
term _em_imaging.electron_dose
(https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_em_imaging.electron_dose.html)
defined as "The electron dose received by the specimen (electrons per
square angstrom)." where the units are those of flux density and not
dose.

The definitions given below arose from a lengthy discussion within the
electron diffraction community (and are supported by the cited
literature reference to RADDOSE, which has DOI
https://doi.org/10.1002/pro.5005).

Regards
Brian


save_diffrn.flux_density

     _definition.id                '_diffrn.flux_density'
     _definition.update            2024-12-02
     _description.text
;
     Flux density of radiation incident at the crystal.

     Reference: Dickerson, J. L., McCubbin, P. T. N., Brooks-Bartlett,
     J. C. & Garman, E. F. (2024). Doses for X-ray and electron
     diffraction: New features in RADDOSE-3D including intensity decay
     models. Protein Sci. 33, e5005.
;
     _name.category_id             diffrn
     _name.object_id               flux_density
     _type.purpose                 Number
     _type.source                  Recorded
     _type.container               Single
     _type.contents                Real
     _enumeration.range            0.0:
     _method.purpose               Definition
     _method.expression
;
     If      (_diffrn_radiation.probe == "neutron")
                                 _units.code =
"neutrons_per_millimetre_squared"
     Else If (_diffrn_radiation.probe == "electron")
                                 _units.code =
"electrons_per_angstrom_squared"
     Else                        _units.code =
"photons_per_millimetre_squared"
;
save_

save_diffrn.total_dose

     _definition.id                '_diffrn.total_dose'
     _definition.update            2024-12-02
     _description.text
;
     Total radiation dose absorbed by the crystal during the diffraction
     experiment.

     Reference: Dickerson, J. L., McCubbin, P. T. N., Brooks-Bartlett,
     J. C. & Garman, E. F. (2024). Doses for X-ray and electron
     diffraction: New features in RADDOSE-3D including intensity decay
     models. Protein Sci. 33, e5005.
;
     _name.category_id             diffrn
     _name.object_id               total_dose
     _type.purpose                 Number
     _type.source                  Recorded
     _type.container               Single
     _type.contents                Real
     _enumeration.range            0.0:
     _units.code                   megagray

save_

save_diffrn.total_exposure_time

     _definition.id                '_diffrn.total_exposure_time'
     _definition.update            2024-12-02
     _description.text
;
     Total time the crystal was exposed during the diffraction experiment.
;
     _name.category_id             diffrn
     _name.object_id               total_exposure_time
     _type.purpose                 Number
     _type.source                  Recorded
     _type.container               Single
     _type.contents                Real
     _enumeration.range            0.0:
     _units.code                   minutes

save_

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Dr. Lukas Palatinus
Laboratory of Electron Crystallography
Department of Structure Analysis
Institute of Physics of the CAS
Na Slovance 2
182 21 Prague 8
Czechia