Literature DB >> 34747533

DIALS as a toolkit.

Graeme Winter1, James Beilsten-Edmands1, Nicholas Devenish1, Markus Gerstel1, Richard J Gildea1, David McDonagh2, Elena Pascal1, David G Waterman2,3, Benjamin H Williams1, Gwyndaf Evans1,4.   

Abstract

The DIALS software for the processing of X-ray diffraction data is presented, with an emphasis on how the suite may be used as a toolkit for data processing. The description starts with an overview of the history and intent of the toolkit, usage as an automated system, command-line use, and ultimately how new tools can be written using the API to perform bespoke analysis. Consideration is also made to the application of DIALS to techniques outside of macromolecular X-ray crystallography.
© 2021 Diamond Light Source Ltd. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.

Entities:  

Keywords:  X-ray crystallography; methods development; open source; software

Mesh：

Year:  2021        PMID： 34747533      PMCID： PMC8740827          DOI： 10.1002/pro.4224

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.993


  23 in total

1.  The finer things in X-ray diffraction data collection.

Authors:  J W Pflugrath
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-10

2.  Breaking the indexing ambiguity in serial crystallography.

Authors:  Wolfgang Brehm; Kay Diederichs
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-12-24

3.  DIALS as a toolkit.

Authors:  Graeme Winter; James Beilsten-Edmands; Nicholas Devenish; Markus Gerstel; Richard J Gildea; David McDonagh; Elena Pascal; David G Waterman; Benjamin H Williams; Gwyndaf Evans
Journal:  Protein Sci       Date:  2021-11-24       Impact factor: 6.993

Review 4.  Scaling and assessment of data quality.

Authors:  Philip Evans
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14

5.  New Python-based methods for data processing.

Authors:  Nicholas K Sauter; Johan Hattne; Ralf W Grosse-Kunstleve; Nathaniel Echols
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-18

6.  Diffraction-geometry refinement in the DIALS framework.

Authors:  David G Waterman; Graeme Winter; Richard J Gildea; James M Parkhurst; Aaron S Brewster; Nicholas K Sauter; Gwyndaf Evans
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-03-30       Impact factor: 7.652

7.  Macromolecular crystallography using microcrystal electron diffraction.

Authors:  Max T B Clabbers; Hongyi Xu
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-02-17       Impact factor: 7.652

8.  Performance of single-photon-counting PILATUS detector modules.

Authors:  P Kraft; A Bergamaschi; Ch Broennimann; R Dinapoli; E F Eikenberry; B Henrich; I Johnson; A Mozzanica; C M Schlepütz; P R Willmott; B Schmitt
Journal:  J Synchrotron Radiat       Date:  2009-04-07       Impact factor: 2.616

9.  New methods for indexing multi-lattice diffraction data.

Authors:  Richard J Gildea; David G Waterman; James M Parkhurst; Danny Axford; Geoff Sutton; David I Stuart; Nicholas K Sauter; Gwyndaf Evans; Graeme Winter
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-09-27

10.  The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment - Olex2 dissected.

Authors:  Luc J Bourhis; Oleg V Dolomanov; Richard J Gildea; Judith A K Howard; Horst Puschmann
Journal:  Acta Crystallogr A Found Adv       Date:  2015-01-01       Impact factor: 2.290
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  6 in total

Review 1.  Electron Diffraction of 3D Molecular Crystals.

Authors:  Ambarneil Saha; Shervin S Nia; José A Rodríguez
Journal:  Chem Rev       Date:  2022-08-15       Impact factor: 72.087

2.  DIALS as a toolkit.

Authors:  Graeme Winter; James Beilsten-Edmands; Nicholas Devenish; Markus Gerstel; Richard J Gildea; David McDonagh; Elena Pascal; David G Waterman; Benjamin H Williams; Gwyndaf Evans
Journal:  Protein Sci       Date:  2021-11-24       Impact factor: 6.993

3.  Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine.

Authors:  Tika R Malla; Lennart Brewitz; Dorian-Gabriel Muntean; Hiba Aslam; C David Owen; Eidarus Salah; Anthony Tumber; Petra Lukacik; Claire Strain-Damerell; Halina Mikolajek; Martin A Walsh; Christopher J Schofield
Journal:  J Med Chem       Date:  2022-05-12       Impact factor: 8.039

4.  xia2.multiplex: a multi-crystal data-analysis pipeline.

Authors:  Richard J Gildea; James Beilsten-Edmands; Danny Axford; Sam Horrell; Pierre Aller; James Sandy; Juan Sanchez-Weatherby; C David Owen; Petra Lukacik; Claire Strain-Damerell; Robin L Owen; Martin A Walsh; Graeme Winter
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-05-18       Impact factor: 5.699

5.  Structural basis for proton coupled cystine transport by cystinosin.

Authors:  Mark Löbel; Sacha P Salphati; Kamel El Omari; Armin Wagner; Stephen J Tucker; Joanne L Parker; Simon Newstead
Journal:  Nat Commun       Date:  2022-08-17       Impact factor: 17.694

6.  Fixed-target serial crystallography at the Structural Biology Center.

Authors:  Darren A Sherrell; Alex Lavens; Mateusz Wilamowski; Youngchang Kim; Ryan Chard; Krzysztof Lazarski; Gerold Rosenbaum; Rafael Vescovi; Jessica L Johnson; Chase Akins; Changsoo Chang; Karolina Michalska; Gyorgy Babnigg; Ian Foster; Andrzej Joachimiak
Journal:  J Synchrotron Radiat       Date:  2022-08-17       Impact factor: 2.557
  6 in total

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