Make wavelength description independent of diffraction experiment #19
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added 2 commits
November 12, 2024 14:31
…nmental conditions This change means that the list of wavelengths and associated radiation production details are specified independent of the sample environment. For example, a multi-temperature data set would not require restating the wavelength for every distinct temperature.
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Note this extended pdCIF example shows how this looks in practice. The first data block describes the radiation source, and that |
vaitkus
reviewed
Dec 12, 2024
multi_block_core.dic
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| @@ -124,19 +144,20 @@ save_DIFFRN_RADIATION | |||
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| _name.category_id DIFFRACTION | |||
| _name.object_id DIFFRN_RADIATION | |||
| _category_key.name '_diffrn_radiation.diffrn_id' | |||
| _category_key.name '_diffrn_radiation.id' | |||
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| save_ | |||
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| save_diffrn_radiation.diffrn_id | |||
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Maybe this item should be removed altogether instead of deprecating it?
Arguments in favour of removal:
- This item was only recently added to this dictionary.
- There are already data items with the same name in the mmCIF and the imgCIF dictionaries so deprecating them here might lead to some confustion.
- The item is no longer referenced as a category key so the intended use case in general is a bit unclear.
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I've removed the definition as suggested.
This is defined in mmCIF.dic, so is available if someone really wants it. However, it does not fit into our concept of associating a single radiation source with a particular experiment; instead it associates a particular experiment with a particular radiation source, which can only make sense when there is a one-to-one relationship between source and experiment. As many measurements can be performed on a single source, this dataname will rarely be useful.
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Fixes issue #505, alternative to #18 .
This is an alternative way of associating more than one wavelength with a diffraction experiment that goes a bit deeper than #18.
DIFFRN_RADIATIONbecomes independent ofDIFFRNand thenDIFFRNincludes an explicit pointer to_diffrn_radiation.id.The advantage of this approach, apart from the ability to specify multiple wavelengths as in #18 , is that radiation characteristics need be provided only once for multiple measurements using the same source. For example a multi-temperature experiment (imagine 100 temperature measurements) need only set the value of
_diffrn.diffrn_radiation_idin thediffrncategory of each measurement, instead of respecifying everything inDIFFRN_RADIATIONandDIFFRN_RADIATION_WAVELENGTHfor every temperature.The drawback is that mmCIF already has defined
_diffrn_radiation.diffrn_id, which this PR deprecates. As this data name has never appeared in a released core dictionary, non mmCIF software does not output it and will not try to interpret it if handed an mmCIF file. It can still be given a well-defined value if there is only one set of diffraction conditions and one source of radiation.