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MX raw image data formats, metadata and validation

IUCr XXV for Prague, CZ has been postponed from August 2020 until August 2021. The Day-0 Workshop on MX raw image data formats, metadata and validation is in two editions:

As an e-meeting via BlueJeans on Saturday, 22 August 2020, from 9 am until 3 pm, Prague Time (GMT+2) which is 1 hour later than London time (8 am until 2 pm), 6 hours later than New York City time (3 am until 9 am), which has been help and is reported on below, and

As a face-to-face Day-0 workshop to be held in Prague on Saturday, 14 August 2021.

This is a report for the 22 August 2020 e-workshop on MX raw image data formats, metadata and validation. The registered participants were:

Registered Participants

Jun Aishima Brookhaven National Lab jaishima at bnl dot gov
Alun Ashton Paul Scherrer Institut alun dot ashtonat psi dot ch
Oskar Aurelius MAX IV Laboratory oskar dot aureliusat maxiv dot lu dot se
Frances C. Bernstein Bernstein + Sons fcb at bernstein-plus-sons dot com
Herbert J. Bernstein Ronin Institute for Independent Scholarship,c/o NSLS-II BNL yayahjb at gmail dot com
Gleb Bourenkov EMBL Hamburg gleb at embl-hamburg dot de
Aaron Brewster LBL asbrewster at lbl dot gov
Gerard Bricogne Global Phasing Ltd. gb10 at globalphasing dot com
Sandor Brockhauser European XFEL sandor dot brockhauser at xfel dot eu
Tom Caradoc-Davies Australian Synchrotron -- ANSTO thomasc at ansto dot gov dot au
Scott Classen ALS -- Berkeley National Laboratory sclassen at lbl dot gov
Ian Clifton Oxford University ian dot clifton at chem dot ox dot ac dot uk
Gregg Crichlow RCSB Protein Data Bank gc663@iqb.rutgers.edu at iqb dot rutgers dot edu
Vikram Dalal Indian Institute of Technology Roorkee vikram dot dalal dot 37 at gmail dot com
Fabio Dall'Antonia European XFEL fabio dot dall dot antonia at xfel dot eu
Poonam Dhankhar Department of Biotechnology, Indian Institute of Technology Roorkee dhankharp16 at gmail dot com
Daniel Eriksson Australian Synchrotron -- ANSTO daniele dot eriksson at ansto dot gov dot au
Andreas Förster DECTRIS Ltd andreas dot foerster at dectris dot com
Luca Gelisio, Center for Free-Electron Laser Science, DESY luca dot gelisio at cfel dot de
Carlotta Giacobbe ESRF carlotta dot giacobbe at gmail dot com
Andy Götz ESRF andy dot gotz at esrf dot fr
David Hall Diamond Light Source david dot hall at diamond dot ac dot uk
Paul Hathaway Diamond Light Source paul dot hathaway at diamond dot ac dot uk
John Helliwell School of Chemistry, The University of Manchester, UK john dot helliwell at manchester dot ac dot uk
Natalie Johnson CCDC njohnson at ccdc dot cam dot ac dot uk
Wonchull Kang University of California Irvine w dot kang at uci dot edu
Wei-Chun Kao University of Freiburg wei-chun dot kao at biochemie dot uni-freiburg dot de
Rajnandani Kashyap CSIR- Indian Institute of Chemical Technology, Hyderabad, India kashyap dot rajnandani at gmail dot com
Kong Wai-Po The Hong Kong Polytechnic University wai-po-ball dot kong at connect dot polyu dot hk
Dale Kreitler CBMS, NSLS-II, BNL dkreitler at bnl dot gov
Loes M. J. Kroon-Batenburg Bijvoet Center for Biomolecular Research, Utrecht University l dot m dot j dot kroon-batenburg at uu dot nl
Filip Leonarski PSI filip dot leonarski at psi dot ch
Filipe Maia Uppsala University filipe at xray dot bmc dot uu dot se
Brian McMahon IUCr bm at iucr dot org
Valerio Mariani SLAC National Accelerator Laboratory valmar at slac dot stanford dot edu
Jie Nan MAX IV Laboratory jie dot nan at maxiv dot lu dot se
Marina Nikolova EMBL, Hamburg nikolova at embl-hamburg dot de
Majid Ounsy SOLEIL Synchrotron majid dot ounsy at synchrotron-soleil dot fr
Evgenii Osipov KU Leuven e dot m dot osipov at gmail dot com
Jason Price ANSTO -- Melbourne jasonp at ansto dot gov dot au
Daniel Salvat ALBA Synchrotron (Barcelona) dsalvat at cells dot es
Gianluca Santoni ESRF gianluca dot santoni at esrf dot fr
Thomas Schneider EMBL Hamburg and DESY thomas dot schneider at embl-hamburg dot de
Irwin Selvam University of Manchester irwin dot selvam at postgrad dot manchester dot ac dot uk
Kate Mary Louise Smith PSI kate dot smith at psi dot ch
S. Sriram Indian Institute of Science hypowergravity at gmail dot com
Amy Thompson School of Chemistry and Molecular Biosciences,
The University of Queensland
amy dot thompson2 at uq dot net dot au
Andrew Thompson SOLEIL Synchrotron andrew dot thompson at synchrotron-soleil dot fr
Alexandra Tolstikova DESY alexandra dot tolstikova at desy dot de
Sameer Velankar PDB-e sameer at ebi dot ac dot uk
Clemens Vonrhein Global Phasing Ltd., Cambridge, UK vonrhein at globalphasing dot com
Suzanna Ward Cambridge Crystallographic Data Centre (CCDC) ward at ccdc dot cam dot ac dot uk
John Westbrook RCSB, Protein Data Bank john dot westbrook at rcsb dot org
Ben Williams Diamond Light Source ben dot williams at diamond dot ac dot uk
Jon Wright ESRF wright at esrf dot fr
Smita Yadav Regional Centre for biotechnology, Haryana-121001. smita at rcb dot res dot in

The most important background information for the 2020 edition is the Gold Standard paper, [Herbert J. Bernstein, Andreas Förster, Asmit Bhowmick, Aaron S. Brewster, Sandor Brockhauser, Luca Gelisio, David R. Hall, Filip Leonarski, Valeria Mariani, Gianluca Santoni, Clemens Vonrhein, Graeme Winter, "Gold Standard for macromolecular crystallography diffraction data," IUCrJ 7, no. 5 (2020)] https://doi.org/10.1107/S2052252520008672

The talks linked to this report and this edited chat provide a great deal of information on the the state of work and issues related to using this standard. The following discussion points seem worth highlighting. Our thanks to John Helliwell in providing notes on these subjects.

It is clear from the talks and the discussion that the Gold Standard as it now exists is useful, but additional documentation and examples of more use cases are needed. We plan on more discussions in Fall 2020 and Spring 2021 and to have much to report in Prague at IUCr XXV in summer 2021.


Saturday, 22 August 2020
New York
9:00 -- 9:15
8:00 -- 8:15
3:00 -- 3:15
Set up for BlueJeans, test connections15
Session 1 Introduction to the Gold Standard
9:15 -- 9:45
8:15 -- 8:45
3:15 -- 3:45
Loes Kroon-BatenburgFAIR and MX Raw Data pdf30yes
9:45 -- 10:15
8:45 -- 9:15
3:45 -- 4:15
Herbert J Bernstein
(Ronin Institute)
MX raw data formats and the Gold Standard pdf 30yes
10:15 -- 10:30
9:15 -- 9:30
4:15 -- 4:30
Coffee break (bring your own coffee, tea or other refreshments)15
Session 2Stream to Gold Standard - Working with FAIR data
10:30 -- 10:45
9:30 -- 9:45
4:30 -- 4:45
Andreas Förster
Stream2 and FileWriter2 pdf 15yes
10:55 -- 11:10
9:55 -- 10:10
4:55 -- 5:10
Paul Hathaway (DLS)
Ben Williams (DLS)
The Gold Standard at DLS pdf 15yes
11:10 -- 11:25
10:10 -- 10:25
5:10 -- 5:25
Filip Leonarski
The Gold Standard at PSI pdf 15yes
11:25 -- 11:35
10:25 -- 10:35
5:25 -- 5:35
break (bring your own coffee, tea or other refreshments) 10
11:35 -- 11:50
10:35 -- 10:50
5:35 -- 5:50
Dale Kreitler
The Gold Standard at NSLS-II pdf 15yes
11:50 -- 12:05
10:50 -- 11:05
5:50 -- 6:05
Jie Nan
The MX Data at Max IV pdf 15yes
12:05 -- 12:30
11:05 -- 11:30
6:05 -- 6:30
Clemens Vonrhein
(Global Phasing)
Requirements of automatic processing pdf 25yes
12:30 -- 12:55
11:30 -- 11:55
6:30 -- 6:55
Sameer Velankar (PDB-e) How can PDB submission be made more automatic pdf 25yes
12:55 -- 13:30
11:55 -- 12:30
6:55 -- 7:30
Lunch break (bring your own lunch or breakfast ..., as appropriate to your time zone)35
Session 3 The future of the Gold Standard
13:30 -- 13:50
12:30 -- 12:50
7:30 -- 7:50
Aaron Brewster
The Gold Standard at XFELs pdf 20yes
13:50 -- 14:10
12:50 -- 13:10
7:50 -- 8:10
Jason Price
(ANSTO -Melbourne (Australian Synchrotron)) and
Natalie Johnson
HDR Detectors and Chemical Crystallography at
the Australian Synchrotron MX Beamlines
Synchrotron Data in the CSD pdf
14:10 -- 15:00
13:15 -- 14:00
8:10 -- 9:00
Open discussion
What metadata are lacking at the moment?
What problems are we envisioning?