Evidence map›Paper›PMID 39091818›Full record

ArticlebioRxiv : the preprint server for biology2024

Laue-DIALS: open-source software for polychromatic X-ray diffraction data.

Rick A Hewitt, Kevin M Dalton, Derek Mendez, Harrison K Wang, Margaret A Klureza, Dennis E Brookner, Jack B Greisman, David McDonagh, Vukica Šrajer, Nicholas K Sauter and 2 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

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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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Rick A HewittDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138.ORCID 0000-0002-5444-8826
Kevin M DaltonLinac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA.ORCID 0000-0001-9396-085X
Derek MendezSLAC National Accelerator Laboratory, Menlo Park, CA 94025.ORCID 0000-0002-2269-0060
Harrison K WangDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138.ORCID 0000-0003-4275-9472
Margaret A KlurezaDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.ORCID 0000-0001-5774-1297
Dennis E BrooknerDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138.ORCID 0000-0003-2827-4743
Jack B GreismanDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138.ORCID 0000-0002-6394-2658
David McDonaghScience and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, OX11 0FA, United Kingdom.ORCID 0000-0003-0025-138X
Vukica ŠrajerBioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA.ORCID 0000-0003-0710-290X
Nicholas K SauterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA.ORCID 0000-0003-2786-6552
Aaron S BrewsterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA.ORCID 0000-0002-0908-7822
Doeke R HekstraDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138.ORCID 0000-0003-2332-9223

Funding

Identifying Principles of Protein Mechanics by Applying Force and Observing MotionDP2GM141000 · NIGMS · HARVARD UNIVERSITY · PI HEKSTRA, DOEKE ROMKE · 2020 to 2020
$2.4M
Cctbx.xfel: Serial crystallography computational methods aimed at biomolecular functionR35GM151988 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI NICHOLAS K SAUTER · 2024 to 2026
$2.2M
NIGMS NIH HHS DP2 GM141000NIGMS NIH HHS R35 GM151988Wellcome Trust
6 · The paper itself

Abstract

Most X-ray sources are inherently polychromatic. Polychromatic ("pink") X-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during exposure-ideal conditions for time-resolved applications. Analysis of such data is complicated, however, causing most X-ray facilities to discard >99% of X-ray photons to obtain monochromatic data. Key challenges in analyzing polychromatic diffraction data include lattice searching, indexing and wavelength assignment, correction of measured intensities for wavelength-dependent effects, and deconvolution of harmonics. We recently described an algorithm, Careless, that can perform harmonic deconvolution and correct measured intensities for variation in wavelength when presented with integrated diffraction intensities and assigned wavelengths. Here, we present Laue-DIALS, an open-source software pipeline that indexes and integrates polychromatic diffraction data. Laue-DIALS is based on the dxtbx toolbox, which supports the DIALS software commonly used to process monochromatic data. As such, Laue-DIALS provides many of the same advantages: an open-source, modular, and extensible architecture, providing a robust basis for future development. We present benchmark results showing that Laue-DIALS, together with Careless, provides a suitable approach to the analysis of polychromatic diffraction data, including for time-resolved applications.

Identifiers

PMID39091818
PMCPMC11291052

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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.