Aquarium: an automatic data-processing and experiment information management system for biological macromolecular crystallography beamlines

被引：83

作者：

Yu, Feng ^{[1
]}

Wang, Qisheng ^{[1
]}

Li, Minjun ^{[1
]}

Zhou, Huan ^{[1
]}

Liu, Ke ^{[1
]}

Zhang, Kunhao ^{[1
]}

Wang, Zhijun ^{[1
]}

Xu, Qin ^{[1
]}

Xu, Chuanyan ^{[1
]}

Pan, Qiangyan ^{[1
]}

He, Jianhua ^{[1
]}

机构：

[1] Chinese Acad Sci, Shanghai Inst Appl Phys, Div Life Sci, 239 Zhangheng Rd, Shanghai 201203, Peoples R China

来源：

JOURNAL OF APPLIED CRYSTALLOGRAPHY | 2019年 / 52卷 / 02期

基金：

中国国家自然科学基金;

关键词：

macromolecular crystallography beamlines; single-wavelength anomalous diffraction; data reduction; SAD phasing; experiment information management; DATA-ACQUISITION; DATA-COLLECTION; SOFTWARE; DETECTOR; MODEL; TOOL; ICE;

D O I：

10.1107/S1600576719001183

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

With the popularity of hybrid pixel array detectors, hundreds of diffraction data sets are collected at a biological macromolecular crystallography (MX) beamline every day. Therefore, the manual processing and recording procedure will be a very time-consuming and error-prone task. Aquarium is an automatic data processing and experiment information management system designed for synchrotron radiation source MX beamlines. It is composed of a data processing module, a daemon module and a web site module. Before experiments, the sample information can be registered into a database. The daemon module will submit data processing jobs to a high-performance cluster as soon as the data set collection is completed. The data processing module will automatically process data sets from data reduction to model building if the anomalous signal is available. The web site module can be used to monitor and inspect the data processing results.

引用

页码：472 / 477

页数：6

共 33 条

[1] Methods used in the structure determination of bovine mitochondrial F-1 ATPase [J].

Abrahams, JP ;

Leslie, AGW .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1996, 52 :30-42

[2] THE CCP4 SUITE - PROGRAMS FOR PROTEIN CRYSTALLOGRAPHY [J].

BAILEY, S .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1994, 50 :760-763

[3] EIGER detector: application in macromolecular crystallography [J].

Casanas, Arnau ;

Warshamanage, Rangana ;

Finke, Aaron D. ;

Panepucci, Ezequiel ;

Olieric, Vincent ;

Noell, Anne ;

Tampe, Robert ;

Brandstetter, Stefan ;

Foerster, Andreas ;

Mueller, Marcus ;

Schulze-Briese, Clemens ;

Bunk, Oliver ;

Wang, Meitian .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2016, 72 :1036-1048

[4] The Buccaneer software for automated model building.: 1.: Tracing protein chains [J].

Cowtan, Kevin .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2006, 62 :1002-1011

[5] Recent developments in classical density modification [J].

Cowtan, Kevin .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2010, 66 :470-478

[6] ISPyB: an information management system for synchrotron macromolecular crystallography [J].

Delageniere, Solange ;

Brenchereau, Patrice ;

Launer, Ludovic ;

Ashton, Alun W. ;

Leal, Ricardo ;

Veyrier, Stephanie ;

Gabadinho, Jose ;

Gordon, Elspeth J. ;

Jones, Samuel D. ;

Levik, Karl Erik ;

McSweeney, Sean M. ;

Monaco, Stephanie ;

Nanao, Max ;

Spruce, Darren ;

Svensson, Olof ;

Walsh, Martin A. ;

Leonard, Gordon A. .

BIOINFORMATICS, 2011, 27 (22) :3186-3192

[7] Features and development of Coot [J].

Emsley, P. ;

Lohkamp, B. ;

Scott, W. G. ;

Cowtan, K. .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2010, 66 :486-501

[8] How good are my data and what is the resolution? [J].

Evans, Philip R. ;

Murshudov, Garib N. .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2013, 69 :1204-1214

[9] An introduction to data reduction: space-group determination, scaling and intensity statistics [J].

Evans, Philip R. .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2011, 67 :282-292

[10] SynchWeb: a modern interface for ISPyB [J].

Fisher, S. J. ;

Levik, K. E. ;

Williams, M. A. ;

Ashton, A. W. ;

McAuley, K. E. .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2015, 48 :927-932

← 1 2 3 4 →