Dear CCP4 list subscribers, Some of you may be interested in giving feedback on the latest draft of the CIF core dictionary. Highlights of the planned release are described at https://github.com/COMCIFS/cif_core/wiki/Release-Notes-for-CIF-CORE-3.2.0 (appended below) and for true CIF afficionados the actual draft dictionary is available at https://github.com/COMCIFS/cif_core/blob/rc-3.2.0/cif_core.dic.
Feedback is best provided via raising a Github issue at https://github.com/COMCIFS/cif_core/issues. Note that this release should in no way affect the mmCIF dictionary, beyond occupying a little more non-pdbx data name territory. Best wishes, James Hester (COMCIFS Chair) ================= # What's New: CIF Core 3.2.0 The following changes are relative to 3.0.13, which was the last released version (June 2020). Only the most significant changes are detailed below; the full list of changes is available [here.](https://github.com/COMCIFS/cif_core/compare/v3.0.13...rc-3.2.0) ## New capabilities ### Author lists Authors should now be identified by an opaque identifier, instead of relying on a unique first name, last name combination. See the `AUDIT_AUTHOR` and `PUBL_AUTHOR` categories. Authors of software that writes CIF files may add `_audit_author.id` and `_publ_author.id` to their output without risking breakage of legacy software. ### Author roles The role that an author played in the experiment can now be specified using the list provided in `_audit_author_role.role`. The current list is: ``` design 'conceived and/or designed the experiment' synthesis 'synthesised the samples' preparation ; prepared the samples for measurement, e.g. crystallised or recrystallised the sample ; characterisation 'performed non-crystallographic measurements on the samples' measurement 'collected and/or reduced diffraction data' analysis 'worked on the structural model' software 'developed bespoke software for specialised data processing and/or analysis' ; submission 'prepared the final CIF file' ``` ### Research support The `AUDIT_AUTHOR_SUPPORT` category has been added to allow description of the sources of support for the work reported in the data file. Sources of support include funding organisations and various awards. ### Elemental composition There is support for recording the elemental composition of the specimen through the addition of `ATOM_ANALYTICAL`, `ATOM_ANALYTICAL_MASS_LOSS`, and `ATOM_ANALYTICAL_SOURCE`. An analyte element and its mass percent can be given, along with the type of the measurement. In some cases, such as XRF, results are given in terms of oxides. In this case, the relevent chemical species and species mass percent can be given, as well as mapped to the relevant analyte element. Furthermore, any mass results, such as through high-temperature treatment, can also be recorded. Lastly, the instrumentation used to collect the elemental composition results can be described. Examples of its use can be found [here]( https://github.com/COMCIFS/cif_core/blob/9aa3e2f49c02bb1401452e0d61260044e82c80eb/cif_core.dic#L19732), [here]( https://github.com/COMCIFS/cif_core/blob/9aa3e2f49c02bb1401452e0d61260044e82c80eb/cif_core.dic#L19955), and [here]( https://github.com/COMCIFS/cif_core/blob/9aa3e2f49c02bb1401452e0d61260044e82c80eb/cif_core.dic#L20151 ). ### Multi-block data sets As specified in [this document]( http://comcifs.github.io/accepted/multi-block-principles), complex data may now be distributed over multiple data blocks. The `Default` way of distributing data, which is backwards-compatible, specifies that items in `Set` categories may only take one value per data block. If more than one data block will contain values from such `Set` categories, key data names must have been assigned in the dictionaries to those `Set` categories. The `DIFFRN` category and related categories have now been equipped with a key data name (`_diffrn.id`) allowing experiments undertaken in varying environmental conditions to be expressed as a single, multi-block data set. Similarly, where data is measured from multiple crystals each crystal can be described separately using data names from the `EXPTL_CRYSTAL` category spread over multiple blocks. Future releases will expand this multi-block capability to further categories. Software that is unaware of such multi-block data sets should still function correctly when passed the contents of any single data block. ### Cells measured under different conditions to the diffraction data In the original CIF core, `_cell_measurement.temperature` and `-_pressure` were provided to allow for the unit cell measurement conditions to differ from those used for the data collection. These data names have now been deprecated. In the usual case that the cell was determined at the same time as the diffraction peaks, cell measurement conditions are indicated using `_diffrn.ambient_temperature` and `_diffrn.ambient_pressure`. In the rare case that the unit cell was measured under different conditions, `_cell_measurement.condition_id` should be set to the `_diffrn.id` of a data block containing the cell measurement conditions provided using `_diffrn.ambient_temperature` and `_diffrn.ambient_pressure`. See _insert link to example_ for an example. ## New data names * `_diffrn_source.beamline` and `_diffrn_source.facility` * `_diffrn.crystal_id`. An identifier for the crystal used to collect the diffraction data. * `_audit_author.id` and `_publ_author.id` (see above). * `_audit_author_role.role` and `_audit_author_role.special_details` (see above) * `_diffrn_refln.intensity_{bg_1, bg_2, net, peak, total}` have been added to allow quantities that are not directly measured counts to be recorded. The `_diffrn_refln.counts_*` data names should only be used when the quantity recorded has a standard uncertainty determined by counting statistics. * `_exptl_absorpt.special_details` for describing absorption corrections where other data names are not sufficient. * data names for more detailed description of elemental compositions: see above. * data names for detailing sources of support for the research: see above. * `_citation.URL` and `_journal_paper.URL` * `_journal.paper_number` and `_journal.paper_pages` * `_model_site.adp_eigenvectors` and `_model_site.adp_eigenvalues`. ## Deprecated data names The following data names should no longer be used. If your software outputs them, you should update to their replacements. If your software reads them, it should be updated to also read the replacements. * `_diffrn_radiation.type` and `_diffrn_radiation.xray_symbol` have been replaced by `_diffrn_radiation_wavelength.type` and `_diffrn_radiation_wavelength.xray_symbol` * `_cell_measurement.temperature`, `pressure` etc... These should almost always be replaced by `_diffrn.ambient_{temperature/pressure/etc.}` See above for more details. ## Removed data names Normally, data names are never removed. The following data names were introduced with the original DDLm dictionaries, but never used in data files, so it was decided that it would be safe to remove them. * `_model_site.adp_eigen_system` * `_citation_author.key` * `_citation_editor.id` ## Minor improvements * Updated author-related definitions to explain how single-name authors are handled. * Fixed various references and URLs * Clarified that `_atom_site.disorder_assembly` and `-_group` also apply to compositional disorder. ## Fixes * Corrected `DIFFRN_STANDARD` to `DIFFRN_STANDARDS` for consistency with DDL1 core dictionary -- ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
