Literature DB >> 34671231

reciprocalspaceship: a Python library for crystallographic data analysis.

Jack B Greisman1, Kevin M Dalton1, Doeke R Hekstra1,2.   

Abstract

Crystallography uses the diffraction of X-rays, electrons or neutrons by crystals to provide invaluable data on the atomic structure of matter, from single atoms to ribosomes. Much of crystallography's success is due to the software packages developed to enable automated processing of diffraction data. However, the analysis of unconventional diffraction experiments can still pose significant challenges - many existing programs are closed source, sparsely documented, or challenging to integrate with modern libraries for scientific computing and machine learning. Described here is reciprocalspaceship, a Python library for exploring reciprocal space. It provides a tabular representation for reflection data from diffraction experiments that extends the widely used pandas library with built-in methods for handling space groups, unit cells and symmetry-based operations. As is illustrated, this library facilitates new modes of exploratory data analysis while supporting the prototyping, development and release of new methods. © Jack B. Greisman et al. 2021.

Entities:  

Keywords:  Python; X-ray crystallography; data analysis

Year:  2021        PMID: 34671231      PMCID: PMC8493618          DOI: 10.1107/S160057672100755X

Source DB:  PubMed          Journal:  J Appl Crystallogr        ISSN: 0021-8898            Impact factor:   4.868


  18 in total

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Authors:  Shailesh Tripathi; Vukica Srajer; Namrta Purwar; Robert Henning; Marius Schmidt
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2.  scikit-image: image processing in Python.

Authors:  Stéfan van der Walt; Johannes L Schönberger; Juan Nunez-Iglesias; François Boulogne; Joshua D Warner; Neil Yager; Emmanuelle Gouillart; Tony Yu
Journal:  PeerJ       Date:  2014-06-19       Impact factor: 2.984

3.  Structure of a protein photocycle intermediate by millisecond time-resolved crystallography.

Authors:  U K Genick; G E Borgstahl; K Ng; Z Ren; C Pradervand; P M Burke; V Srajer; T Y Teng; W Schildkamp; D E McRee; K Moffat; E D Getzoff
Journal:  Science       Date:  1997-03-07       Impact factor: 47.728

4.  XDS.

Authors:  Wolfgang Kabsch
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-01-22

5.  Electric-field-stimulated protein mechanics.

Authors:  Doeke R Hekstra; K Ian White; Michael A Socolich; Robert W Henning; Vukica Šrajer; Rama Ranganathan
Journal:  Nature       Date:  2016-12-07       Impact factor: 49.962

6.  PHENIX: a comprehensive Python-based system for macromolecular structure solution.

Authors:  Paul D Adams; Pavel V Afonine; Gábor Bunkóczi; Vincent B Chen; Ian W Davis; Nathaniel Echols; Jeffrey J Headd; Li-Wei Hung; Gary J Kapral; Ralf W Grosse-Kunstleve; Airlie J McCoy; Nigel W Moriarty; Robert Oeffner; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger; Peter H Zwart
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-01-22

7.  How good are my data and what is the resolution?

Authors:  Philip R Evans; Garib N Murshudov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-13

8.  Bayesian machine learning improves single-wavelength anomalous diffraction phasing.

Authors:  Maria Jose Garcia-Bonete; Gergely Katona
Journal:  Acta Crystallogr A Found Adv       Date:  2019-10-07       Impact factor: 2.290

Review 9.  Array programming with NumPy.

Authors:  Charles R Harris; K Jarrod Millman; Stéfan J van der Walt; Ralf Gommers; Pauli Virtanen; David Cournapeau; Eric Wieser; Julian Taylor; Sebastian Berg; Nathaniel J Smith; Robert Kern; Matti Picus; Stephan Hoyer; Marten H van Kerkwijk; Matthew Brett; Allan Haldane; Jaime Fernández Del Río; Mark Wiebe; Pearu Peterson; Pierre Gérard-Marchant; Kevin Sheppard; Tyler Reddy; Warren Weckesser; Hameer Abbasi; Christoph Gohlke; Travis E Oliphant
Journal:  Nature       Date:  2020-09-16       Impact factor: 49.962

10.  A tool for visualizing protein motions in time-resolved crystallography.

Authors:  Cecilia Wickstrand; Gergely Katona; Takanori Nakane; Przemyslaw Nogly; Joerg Standfuss; Eriko Nango; Richard Neutze
Journal:  Struct Dyn       Date:  2020-04-01       Impact factor: 2.920

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  2 in total

1.  Native SAD phasing at room temperature.

Authors:  Jack B Greisman; Kevin M Dalton; Candice J Sheehan; Margaret A Klureza; Igor Kurinov; Doeke R Hekstra
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-07-27       Impact factor: 5.699

2.  Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies.

Authors:  Elke De Zitter; Nicolas Coquelle; Paula Oeser; Thomas R M Barends; Jacques-Philippe Colletier
Journal:  Commun Biol       Date:  2022-06-29
  2 in total

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