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New items relevant to radiation damage

  • To: coredmg@iucr.org
  • Subject: New items relevant to radiation damage
  • From: Brian McMahon via coreDMG <coredmg@mailman.iucr.org>
  • Date: Fri, 6 Dec 2024 13:45:44 +0000
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I have been working with the NanED project on new CIF data namesrelevant to electron diffraction, and the suggestion has arisen for anumber of items that allow some assessment of the amount of radiationthat the crystal is subjected to. It seems to me that these terms havemore general application, and so I am posting these suggesteddefinitions 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 radiationprobe. Note also that the terminology regarding amount of radiation isoften confused and confusing. For example, the mmCIF dictionary has aterm _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 persquare angstrom)." where the units are those of flux density and notdose.
The definitions given below arose from a lengthy discussion within theelectron diffraction community (and are supported by the citedliterature reference to RADDOSE, which has DOIhttps://doi.org/10.1002/pro.5005).
RegardsBrian

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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