Category keys needed

[rowlesmr]

Categories missing keys:

• PD_CALIBRATION: I think needs a diffractogram id. It talks about calibrating _pd_meas.detector_id or _pd_meas.position values to Q, energy, angle, etc.
• PD_CHAR is a funny one; even though it is about the specimen, I think I to want a link to diffractogram_id. See also PD_PREP and PD_SPEC.
• PD_PREP: I think this needs to link somehow with PD_SPEC. PD_PREP details the preparation of the material from which the specimen is drawn, whereas PD_SPEC details the actual thing you put in the beam.

[rowlesmr]

also, does anything need a diffrn.id? PD_CALIB_WAVELENGTH has one.

[jamesrhester]

The specimen is already linked to the diffractogram through _pd_diffractogram.spec_id, so I don't think we need to fiddle with PD_SPEC.

PD_CHAR looks to me like you could just have a _pd_char.spec_id as key data name and be done for our purposes as we have no categories corresponding to sample or material. Because there is a _pd_diffractogram.spec_id, diffractogram is indirectly linked to PD_CHAR they both are linked to spec_id.

PD_PREP: this looks like a PD_SAMPLE category because I don't think there are any other data names that refer to sample-specific information as opposed to material or specimen. If we add a key data name to PD_PREP _pd_prep.sample_id we can then link to it from pd_spec.

What is the remaining function of PD_CALIBRATION after the new categories we've introduced? If it has none, we can leave it as a Set category and thereby indicate that it should not be used going forward. If it should be kept, then I think that the easiest thing is to give it a key data name that is a child of _diffractogram.id. I have a niggle with this in that many diffractograms might have the same correction, but on the other hand there is no label for some "grouping" of diffractograms that would allow us to point to anything else, and these corrections do get updated from time to time.

[rowlesmr]

I think this one is done with #133 and #127.

I do need to remind myself on what a diffn.id is for.

[jamesrhester]

diffrn.id is for a set of experimental conditions (see DIFFRN category), which includes wavelength and radiation type. Normally it would be associated with a diffractogram, I'd think.

[rowlesmr]

_diffrn.id has temperature/pressure/environment. Does it also point to DIFFRN_RADIATION_WAVELENGTH? (which is part of DIFFRN_RADIATION, which is part of DIFFRN).

PD_INSTR might need a link to DIFFRN_RADIATION_WAVELENGTH to properly associate wavelengths, and PD_DIFFRACTOGRAM might need a link to _diffrn.id to properly associate temperature/pressure.

[jamesrhester]

So formally, diffrn_radiation_wavelength has a pointer to _diffrn.id as one of its keys. This is done explicitly in mmCIF, if I remember correctly. To my mind the wavelength and environmental conditions can be separated from the instrument geometry, that is, a single geometry can have multiple wavelengths or conditions associated with it. So really it is only necessary to have a link from PD_DIFFRACTOGRAM to DIFFRN, and that will take care of wavelength as well.

I know it is a bit annoying that multiple environmental conditions need to repeat the wavelength value, but that is what we have inherited. Ideally wavelength would not be linked to conditions but we can't undo that now.

[rowlesmr]

diffrn_radiation_wavelength has a pointer to _diffrn.id as one of its keys.

Is that just because DIFFRN_RADIATION_WAVELENGTH is a subcategory of DIFFRN? There isn't a dataitem which is linked to _diffrn.id.

Where can I find a copy of the current mmCIF? All I can find is https://www.ebi.ac.uk/pdbe/docs/documentation/mmcif.html, and that is in the old format.

[jamesrhester]

The current mmCIF is at https://mmcif.wwpdb.org

I misremembered, DIFFRN_RADIATION has a link to _diffrn.id, but the wavelength list does not. So DIFFRN_RADIATION has a (non-key) link to a wavelength identifier from the wavelength list. If you change this wavelength identifier, you need a new _diffrn.id