Online data analysis at the ESRF bioSAXS beamline, BM29

被引：73

作者：

Brennich, Martha Elisabeth ^{[1
]}

Kieffer, Jerome ^{[1
]}

Bonamis, Guillaume ^{[1
]}

Antolinos, Alejandro De Maria ^{[1
,2
]}

Hutin, Stephanie ^{[3
]}

Pernot, Petra ^{[1
]}

Round, Adam ^{[2
,3
,4
]}

机构：

[1] European Synchrotron Radiat Facil, 71 Ave Martyrs,CS 40220, F-38043 Grenoble, France

[2] European Mol Biol Lab, Grenoble Outstn, 71 Ave Martyrs,CS 90181, F-38042 Grenoble, France

[3] Univ Grenoble Alpes, EMBL, CNRS, Unit Virus Host Cell Interact, 71 Ave Martyrs,CS 90181, F-38042 Grenoble, France

[4] Keele Univ, Fac Nat Sci, Keele ST5 5BG, Staffs, England

来源：

JOURNAL OF APPLIED CRYSTALLOGRAPHY | 2016年 / 49卷

关键词：

online data analysis; solution scattering; proteins; X-RAY-SCATTERING; SMALL-ANGLE SCATTERING; SAXS; RESOLUTION; MACROMOLECULES; ACQUISITION; MODELS; !text type='PYTHON']PYTHON[!/text; MASS;

D O I：

10.1107/S1600576715024462

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

High-throughput small-angle X-ray scattering on proteins in solution (bioSAXS) at synchrotron sources is a commonly used technique in structural biology, which relies on highly automated data acquisition. Data reduction and primary analysis for bioSAXS experiments consist of a well defined series of individual tasks, the automation of which allows a first easy assessment of the quality of collected data and the adjustment of collection strategies if necessary. This article describes both the logic and the technical implementation of the automated processing pipeline for bioSAXS data at the ESRF BM29 beamline using the EDNA framework.

引用

页码：203 / 212

页数：10

共 41 条

[1]

Aishima J., 2014, AM CRYST ASS M 24 28

[2] ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments [J].

Antolinos, Alejandro De Maria ;

Pernot, Petra ;

Brennich, Martha E. ;

Kieffer, Jerome ;

Bowler, Matthew W. ;

Delageniere, Solange ;

Ohlsson, Staffan ;

Monaco, Stephanie Malbet ;

Ashton, Alun ;

Franke, Daniel ;

Svergun, Dmitri ;

McSweeney, Sean ;

Gordon, Elspeth ;

Round, Adam .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2015, 71 :76-85

[3] The fast azimuthal integration Python']Python library: pyFAI [J].

Ashiotis, Giannis ;

Deschildre, Aurore ;

Nawaz, Zubair ;

Wright, Jonathan P. ;

Karkoulis, Dimitrios ;

Picca, Frederic Emmanuel ;

Kieffer, Jerome .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2015, 48 :510-519

[4] Cython: The Best of Both Worlds [J].

Behnel, Stefan ;

Bradshaw, Robert ;

Citro, Craig ;

Dalcin, Lisandro ;

Seljebotn, Dag Sverre ;

Smith, Kurt .

COMPUTING IN SCIENCE & ENGINEERING, 2011, 13 (02) :31-39

[5] A customizable software for fast reduction and analysis of large X-ray scattering data sets: applications of the new DPDAK package to small-angle X-ray scattering and grazing-incidence small-angle X-ray scattering [J].

Benecke, Gunthard ;

Wagermaier, Wolfgang ;

Li, Chenghao ;

Schwartzkopf, Matthias ;

Flucke, Gero ;

Hoerth, Rebecca ;

Zizak, Ivo ;

Burghammer, Manfred ;

Metwalli, Ezzeldin ;

Mueller-Buschbaum, Peter ;

Trebbin, Martin ;

Foerster, Stephan ;

Paris, Oskar ;

Roth, Stephan V. ;

Fratzl, Peter .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2014, 47 :1797-1803

[6] Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY) [J].

Blanchet, Clement E. ;

Spilotros, Alessandro ;

Schwemmer, Frank ;

Graewert, Melissa A. ;

Kikhney, Alexey ;

Jeffries, Cy M. ;

Franke, Daniel ;

Mark, Daniel ;

Zengerle, Roland ;

Cipriani, Florent ;

Fiedler, Stefan ;

Roessle, Manfred ;

Svergun, Dmitri I. .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2015, 48 :431-443

[7] Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler (US-SOMO) enhanced SAS module [J].

Brookes, Emre ;

Perez, Javier ;

Cardinali, Barbara ;

Profumo, Aldo ;

Vachette, Patrice ;

Rocco, Mattia .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2013, 46 :1823-1833

[8] Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamline [J].

David, G. ;

Perez, J. .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2009, 42 :892-900

[9] XRDUA: crystalline phase distribution maps by two-dimensional scanning and tomographic (micro) X-ray powder diffraction [J].

De Nolf, Wout ;

Vanmeert, Frederik ;

Janssens, Koen .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2014, 47 :1107-1117

[10] Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching [J].

Du, Pan ;

Kibbe, Warren A. ;

Lin, Simon M. .

BIOINFORMATICS, 2006, 22 (17) :2059-2065

← 1 2 3 4 5 →