Evidence map›Paper›PMID 37584427›Full record

ArticleActa crystallographica. Section D, Structural biology2023

Correcting systematic errors in diffraction data with modern scaling algorithms.

Luis A Aldama, Kevin M Dalton, Doeke R Hekstra

Abstract read
In one paragraph

Article in Acta crystallographica. Section D, Structural biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Article
  2. Article
  3. Robust error calibration for serial crystallography.Acta crystallographica. Section D, Structural biology · 2025
    Article
  4. Article
  5. Article
  6. Scaling and Merging Time-Resolved Laue Data with Variational Inference.bioRxiv : the preprint server for biology · 2024
    Article
  7. Article
  8. Article
  9. High-resolution double vision of the allosteric phosphatase PTP1B.Acta crystallographica. Section F, Structural biology communications · 2024
    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

3 authors.

Luis A AldamaDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.
Kevin M DaltonDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.ORCID 0000-0001-9396-085X
Doeke R HekstraDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.ORCID 0000-0003-2332-9223

Funding

MOLECULAR BIOPHYSICS TRAINING GRANTT32GM008313 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI MURTHY, VENKATESH N · 1989 to 2023
$14.6M
Identifying Principles of Protein Mechanics by Applying Force and Observing MotionDP2GM141000 · NIGMS · HARVARD UNIVERSITY · PI HEKSTRA, DOEKE ROMKE · 2020 to 2020
$2.4M
NIGMS NIH HHS DP2 GM141000NIGMS NIH HHS T32 GM008313NIH HHS DP2-GM141000
6 · The paper itself

Abstract

X-ray diffraction enables the routine determination of the atomic structure of materials. Key to its success are data-processing algorithms that allow experimenters to determine the electron density of a sample from its diffraction pattern. Scaling, the estimation and correction of systematic errors in diffraction intensities, is an essential step in this process. These errors arise from sample heterogeneity, radiation damage, instrument limitations and other aspects of the experiment. New X-ray sources and sample-delivery methods, along with new experiments focused on changes in structure as a function of perturbations, have led to new demands on scaling algorithms. Classically, scaling algorithms use least-squares optimization to fit a model of common error sources to the observed diffraction intensities to force these intensities onto the same empirical scale. Recently, an alternative approach has been demonstrated which uses a Bayesian optimization method, variational inference, to simultaneously infer merged data along with corrections, or scale factors, for the systematic errors. Owing to its flexibility, this approach proves to be advantageous in certain scenarios. This perspective briefly reviews the history of scaling algorithms and contrasts them with variational inference. Finally, appropriate use cases are identified for the first such algorithm, Careless, guidance is offered on its use and some speculations are made about future variational scaling methods.

Indexed as

AlgorithmsResearch DesignBayes TheoremX-Ray Diffractiondeep learningscalingvariational inferenceX-ray crystallography

Identifiers

PMID37584427
PMCPMC10478637

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.