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/
