Evidence map›Paper›PMID 25664746›Full record

ArticleActa crystallographica. Section D, Biological crystallography2015

Data Exploration Toolkit for serial diffraction experiments.

Oliver B Zeldin, Aaron S Brewster, Johan Hattne, Monarin Uervirojnangkoorn, Artem Y Lyubimov, Qiangjun Zhou, Minglei Zhao, William I Weis, Nicholas K Sauter, Axel T Brunger

Abstract read
In one paragraph

Article in Acta crystallographica. Section D, Biological crystallography, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.

0numbers the graph read from it
0cells of the map it votes in
21citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

21 citing papers in PubMed.

  1. Article
  2. Article
  3. bioRxiv : the preprint server for biology · 2025
    Article
  4. Article
  5. Article
  6. Serial crystallography with multi-stage merging of thousands of images.Acta crystallographica. Section F, Structural biology communications · 2022
    Article
  7. xia2.multiplex: a multi-crystal data-analysis pipeline.Acta crystallographica. Section D, Structural biology · 2022
    Article
  8. Article
  9. Journal of applied crystallography · 2019
    Article
  10. A space for lattice representation and clustering.Acta crystallographica. Section A, Foundations and advances · 2019
    Article
  11. How best to use photons.Acta crystallographica. Section D, Structural biology · 2019
    Article
  12. Article
  13. Article
  14. Article
  15. TakeTwo: an indexing algorithm suited to still images with known crystal parameters.Acta crystallographica. Section D, Structural biology · 2016
    Article
  16. Journal of applied crystallography · 2016
    Article
  17. Journal of applied crystallography · 2016
    Article
  18. Recent developments inJournal of applied crystallography · 2016
    Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Oliver B ZeldinDepartment of Molecular and Cellular Physiology, Stanford University, USA.
Aaron S BrewsterPhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Johan HattneJanelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
Monarin UervirojnangkoornDepartment of Molecular and Cellular Physiology, Stanford University, USA.
Artem Y LyubimovDepartment of Molecular and Cellular Physiology, Stanford University, USA.
Qiangjun ZhouDepartment of Molecular and Cellular Physiology, Stanford University, USA.
Minglei ZhaoDepartment of Molecular and Cellular Physiology, Stanford University, USA.
William I WeisDepartment of Molecular and Cellular Physiology, Stanford University, USA.
Nicholas K SauterPhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Axel T BrungerDepartment of Molecular and Cellular Physiology, Stanford University, USA.

Funding

X-ray Absorption Spectroscopy (XAS) pp.711-759P41GM103393 · NIGMS · STANFORD UNIVERSITY · PI HODGSON, KEITH O · 2012 to 2019
$30.6M
Realizing New Horizons in X-ray Crystallography Data ProcessingR01GM095887 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI SAUTER, NICHOLAS K · 2011 to 2014
$1.5M
Towards real-time XFEL data reduction with CCTBXR01GM102520 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI SAUTER, NICHOLAS K · 2012 to 2015
$1.4M
Howard Hughes Medical InstituteNIGMS NIH HHS GM095887NIGMS NIH HHS GM102520NIGMS NIH HHS P41 GM103393NIGMS NIH HHS P41GM103393NIGMS NIH HHS R01 GM095887NIGMS NIH HHS R01 GM102520
6 · The paper itself

Abstract

Ultrafast diffraction at X-ray free-electron lasers (XFELs) has the potential to yield new insights into important biological systems that produce radiation-sensitive crystals. An unavoidable feature of the `diffraction before destruction' nature of these experiments is that images are obtained from many distinct crystals and/or different regions of the same crystal. Combined with other sources of XFEL shot-to-shot variation, this introduces significant heterogeneity into the diffraction data, complicating processing and interpretation. To enable researchers to get the most from their collected data, a toolkit is presented that provides insights into the quality of, and the variation present in, serial crystallography data sets. These tools operate on the unmerged, partial intensity integration results from many individual crystals, and can be used on two levels: firstly to guide the experimental strategy during data collection, and secondly to help users make informed choices during data processing.

Indexed as

Cluster AnalysisCrystallizationCrystallography, X-RayElectronic Data ProcessingLasersTime FactorsData Exploration Toolkitultrafast diffractionX-ray free-electron lasers

Identifiers

PMID25664746
PMCPMC4321488

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.