Dear Kevin,
I’ve just been working through the issue myself of how to deposit both the pruned data needed to reproduce the refinement and the unmassaged data. The advice I got from the people at PDBe was to prepare an mmCIF file with two reflection loops. The validation pipeline expects the first one to contain the data actually used in refinement, so I prepared one in which the second loop contained the full set of intensities. It should also be possible to have a third loop containing unmerged original-index (but probably scaled) intensity data, and this would be a good intermediate ground between the worst option of just depositing French & Wilson (truncate) amplitudes and the ideal-world case of depositing the raw diffraction images.
Like you, I used the sf-tool at wwPDB, but I’ve just double-checked and the mmCIF file I got has the same free flags for both reflection loops. In case this helps to narrow down why you had a problem and I didn’t, the data I submitted were in a single MTZ file, and the R-free flags had been prepared with the CCP4 convention, with values from 0 to 19, and not a binary convention with just values of 0 and 1.
I’ve also been wondering about when you get to label the different intensity sets! The mmCIF standard doesn’t have data types that distinguish different kinds of observed intensities. We haven’t yet deposited the structure with the data, and I’ve been hoping that you’re asked to provide labels during the deposition process. Perhaps someone from one of the wwPDB sites, or someone who has gotten as far as depositing such data, can comment!
Best wishes,
Randy Read
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
> On 26 Sep 2018, at 19:34, Kevin Jude <[log in to unmask]> wrote:
>
> I am preparing to deposit several structures that I refined against anisotropic data that I truncated with STARANISO. I will of course be depositing the original data with spherical resolution limits, but it seems that I should also deposit the ellipsoidally truncated data that I actually refined against. To be clear, these are the same dataset but in the second case the unmerged reflections have been rescaled and I/SIGIs that fall outside the ellipsoid are set to empty values. I have a technical problem with preparing the mmcif and a broader question about presenting the data.
>
> I've tried to create an mmcif file from my mtz using http://sf-tool.wwpdb.org, treating the two sets of I/sigI as two datasets. For some reason, in the output file the test set flags are reversed for the second "dataset" (whichever I choose to be second); ie, o becomes f and f becomes o. This is a technical problem that I can correct with a text editor, but still irritating.
>
> More importantly, is there a way to distinguish in the file between the spherically complete dataset and the truncated dataset that was used in refinement in a way that is useful to future users? I have not worked with mmcif before and am not sure what column names are permissible, nor what would be recognizable to other users or software. I'm interested to hear the thoughts and experiences of the community on this.
>
> Best wishes
> Kevin
>
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
>
>
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