Hi Marcin, Thanks for your inputs. I wonder why the PDB doesn’t allow to submit two separate mtz files, one from data processing and one from refinement with map coefficients. It would be very straightforward for depositions. I guess there must be a valid reason for not allowing that.
BW, D > On 14 Jan 2022, at 18:52, Marcin Wojdyr <woj...@gmail.com> wrote: > > 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/ ######################################################################## 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/
