_pdbx_diffrn_merge_stat: missing items

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wwPDB PDBx/mmCIF Dictionary

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_pdbx_diffrn_merge_stat: missing items #23

Open CV-GPhL opened 3 years ago

CV-GPhL commented 3 years ago

_pdbx_diffrn_merge_stat.Rmeas_all Redundancy-independant merging R factor value Rmeas, for merging all intensities in this data set. K. Diederichs and P.A. Karplus (1997). Improved R-factors for diffraction data analysis in macromolecular crystallography. Nature Struct. Biol. 4, 269-275. M.S. Weiss and R. Hilgenfeld (1997) On the use of the merging R-factor as a quality indicator for X-ray data. J. Appl. Crystallogr. 30, 203-205.
_pdbx_diffrn_merge_stat.redundancy The overall redundancy of the merged reflections in this data set.

epeisach commented 3 years ago

This makes sense. Can you clarify if Rmeas_all will be on F or I? The Karplus 1997 paper describes both.

CV-GPhL commented 3 years ago

As far as I can see, any data merging metric would only ever be on intensities. A good reference is [1] - but be aware, that as a result of the data-quality metrics workshop [2] we have been working with both Kay Diederichs and Manfred Weiss (and also Phil Evans) to help resolving any remaining confusion, e.g. about the use of an average versus inverse-variance weighted mean intensity.

[1] Einspahr, H. and Weiss, M. [2012], International Tables for Crystallography, Vol. F, edited by E. Arnold, DM Himmel & MG Rossmann, Chichester: Wiley, chapter Chapter 2.2. Quality indicators in macromolecular crystallography: definitions and applications, pp. 64-74.

[2] https://www.globalphasing.com/DQMW/

dagewa commented 3 years ago

This applies to the diffrn-data-set-extension, not the base dictionary, right? Can we have a "diffrn-data-set-extension" label for such issues?

CV-GPhL commented 3 years ago

Correct ... there is a duplication of this issue at https://github.com/pdbxmmcifwg/diffrn-data-set-extension/issues/10 (where it should have belonged in the first place). Sorry!

We now tend to have v50 issues here and v5-next issues at https://github.com/pdbxmmcifwg/diffrn-data-set-extension.

dagewa commented 3 years ago

Right, makes sense. Thanks!