Then I'm afraid you'd need to first use CAD to combine both mtz files (merged intensities and map coefficients) into one merged mtz file. Or perhaps there is a better way - I don't know. Perhaps ccp4i2 and Ccp4 Cloud can combine MTZ files.
I'll think about supporting multiple merged MTZs in mxdepo.html in the future. Best, Marcin On Fri, 14 Jan 2022 at 17:42, Dom Bellini - MRC LMB <dbell...@mrc-lmb.cam.ac.uk> wrote: > > Hi Marcin, > > This is very helpful, thanks a lot. Ezra and Jasmine from wwPDB have > also replied just to me that they will send me a work around asap; if it > will differ from your method I will post it. > > Can I please also ask you would be the best way to proceed if I would > like to combine, as well as the merged data used for refinement and the > unmerged mtz file, also the mtz output from the refinement software > containing the map coefficients? > > Many thanks, > > D > > On 14/01/2022 16:32, Marcin Wojdyr wrote: > > Dear Dom, > > > > you can upload only a single data file to OneDep. > > Currently, if you want to deposit unmerged data with extensions > > introduced in 2021 (importantly, these extensions include image > > numbers and rotation angles) and if the software that you use doesn't > > output such ready-to-use files, you need to first input two files: > > - merged data that was used for refinement (MTZ or mmCIF) > > - scaled unmerged data (MTZ or XDS_ASCII) > > to this converter: > > https://project-gemmi.github.io/wasm/mxdepo.html > > and then you can upload the resulting cif file to the wwPDB deposition > > system. > > > > Best wishes > > Marcin > > > > On Thu, 13 Jan 2022 at 20:34, Dom Bellini - MRC LMB > > <dbell...@mrc-lmb.cam.ac.uk> wrote: > >> Dear Jasmine, > >> > >> But can we now upload two mtz/mmcif files now for the structure factors? > >> as in, the one from the processing software containing the raw data, as > >> well as the one with the weighted amplitudes and the phases from > >> Refinement software? Or do we still have to use CAD to create a single mtz > >> file and then convert it to mmcif for depostion? Or is there another > >> better way to do it? > >> > >> Many thanks for your help, > >> > >> Dom > >> > >> > >> > >> > >> On 13/01/2022 19:19, Jasmine Young wrote: > >> > >> Dear all, > >> > >> Extensions to the PDBx/mmCIF dictionary for reflection data with > >> anisotropic diffraction limits, for unmerged reflection data, and for > >> quality metrics of anomalous diffraction data are now supported in OneDep. > >> > >> In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group was > >> convened to develop a richer description of experimental data and > >> associated data quality metrics. Members of this Data Collection and > >> Processing Subgroup are all actively engaged in development and support of > >> diffraction data processing software. The Subgroup met virtually for > >> several months discussing, reviewing, and finalizing a new set dictionary > >> content extension that were incorporated into the PDBx/mmCIF dictionary on > >> February 16, 2021. A reference implementation of the new content > >> extensions has been developed by Global Phasing Ltd. > >> > >> These extensions facilitate the deposition and archiving of a broader > >> range of diffraction data, as well as new quality metrics pertaining to > >> these data. These extensions cover three main areas: > >> > >> scaled and merged reflection data that have been processed to take account > >> of diffraction anisotropy, by providing descriptors for that anisotropy, > >> in terms of (1) a parameter-free definition of a cut-off surface by means > >> of a per-reflection “signal” and a threshold value for that signal, and > >> (2) the ellipsoid providing the best fit to the resulting cut-off surface; > >> scaled and unmerged reflection data, by providing extra item definitions > >> aimed at ensuring that such data can be meaningfully re-analysed, and > >> their quality assessed independently from the associated model, after > >> retrieval from the archive; > >> anomalous diffraction data, by adding descriptors for numerous relevant, > >> but previously missing, statistics. > >> > >> The new mmCIF data extensions describing anisotropic diffraction now > >> enable archiving of the results of Global Phasing’s STARANISO program. > >> Developers of other software can make use of them or extend the present > >> definitions to suit their applications. Example files created by autoPROC, > >> BUSTER (version 20210224) and Gemmi that are compliant with the new > >> dictionary extensions are provided in a GitHub repository. > >> > >> These example files, and similarly compliant files produced by other data > >> processing and/or refinement programs, are suitable for direct uploading > >> to the wwPDB OneDep system. Automatic recognition of that compliance, > >> implemented by means of explicit dictionary versioning using the new > >> pdbx_audit_conform record, will avoid unnecessary pre-processing at the > >> time of deposition. This improved OneDep support will ensure a lossless > >> round trip between data processing/refinement in the lab and deposition at > >> the PDB. > >> > >> wwPDB strongly encourages structural biologists to always use the latest > >> versions of structure determination software packages to produce data > >> files for PDB deposition. wwPDB also encourages crystallographers wishing > >> to deposit new structures together with their associated diffraction data > >> to use the software which guarantees consistency between data and final > >> model. This consistency is difficult to achieve when separate diffraction > >> data files and model coordinate files are pieced together a posteriori by > >> ad hoc means. > >> > >> wwPDB also encourages depositors to make their raw diffraction images > >> available from one of the public repositories to allow direct access to > >> the original diffraction image data. > >> > >> > >> -- > >> Regards, > >> > >> Jasmine > >> > >> =========================================================== > >> Jasmine Young, Ph.D. > >> Biocuration Team Lead > >> RCSB Protein Data Bank > >> Research Professor > >> Institute for Quantitative Biomedicine > >> Rutgers, The State University of New Jersey > >> 174 Frelinghuysen Rd > >> Piscataway, NJ 08854-8087 > >> > >> Email: jasm...@rcsb.rutgers.edu > >> Phone: (848)445-0103 ext 4920 > >> Fax: (732)445-4320 > >> =========================================================== > >> > >> > >> ________________________________ > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >> > >> > >> -- > >> Dom Bellini, Xray Crystallography Facility (1S205) > >> MRC Laboratory of Molecular Biology > >> Francis Crick Avenue > >> Cambridge Biomedical Campus > >> Cambridge CB2 0QH > >> Phone 01223 267839 > >> > >> > >> ________________________________ > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > -- > Dom Bellini, Xray Crystallography Facility (1S205) > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge CB2 0QH > Phone 01223 267839 > ######################################################################## 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/
