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Re: New items relevant to radiation damage

  • To: coredmg@iucr.org
  • Subject: Re: New items relevant to radiation damage
  • From: Brian McMahon via coreDMG <coredmg@mailman.iucr.org>
  • Date: Fri, 31 Jan 2025 11:42:00 +0000
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  • Cc: Brian McMahon <bm@iucr.org>, "'Elspeth Garman'" <elspeth.garman@bioch.ox.ac.uk>, palat <palat@fzu.cz>
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I have also run these suggestions past Elspeth Garman (an author of thecited RADDOSE paper), who would be happy to see these items added to thecore dictionary, but she pointed out that the correct units for fluxdensity areelectrons_per_angstrom_squared_per_secondphotons_per_millimetre_squared_per_secondneutrons_per_millimetre_squared_per_second
(The mistake in the draft definitions was mine in wrongly interpretingLukas' original proposal. Thank you, Elspeth.)
If there are no further comments by the end of next week, I will addthese definitions and the new units to the current development versioncore dictionary as a GitHub pull request.
Brian

On 06/12/2024 13:45, Brian McMahon 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_> _______________________________________________coreDMG mailing listcoreDMG@mailman.iucr.orghttps://mailman.iucr.org/cgi-bin/mailman/listinfo/coredmg

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