Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system
Abstract
The calculation of single- and multi-crystal data collection strategies and a data processing pipeline have been tightly integrated into the macromolecular crystallographic data acquisition and beamline control software JBluIce. Both tasks employ wrapper scripts around existing crystallographic software. JBluIce executes scripts through a distributed resource management system to make efficient use of all available computing resources through parallel processing. The JBluIce single-crystal data collection strategy feature uses a choice of strategy programs to help users rank sample crystals and collect data. The strategy results can be conveniently exported to a data collection run. The JBluIce multi-crystal strategy feature calculates a collection strategy to optimize coverage of reciprocal space in cases where incomplete data are available from previous samples. The JBluIce data processing runs simultaneously with data collection using a choice of data reduction wrappers for integration and scaling of newly collected data, with an option for merging with pre-existing data. Data are processed separately if collected from multiple sites on a crystal or from multiple crystals, then scaled and merged. Results from all strategy and processing calculations are displayed in relevant tabs of JBluIce.
- Authors:
-
- Argonne National Lab. (ANL), Lemont, IL (United States)
- Diamond Light Source, Oxfordshire (United Kingdom)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of Michigan, Ann Arbor, MI (United States). Life Sciences Inst. and Dept. of Biological Chemistry.
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1212769
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Applied Crystallography (Online)
- Additional Journal Information:
- Journal Name: Journal of Applied Crystallography (Online); Journal Volume: 47; Journal Issue: 6; Journal ID: ISSN 1600-5767
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; 97 MATHEMATICS AND COMPUTING; automated data processing; multi-crystal data collection strategies; X-ray crystallography; Grid Engine
Citation Formats
Pothineni, Sudhir Babu, Venugopalan, Nagarajan, Ogata, Craig M., Hilgart, Mark C., Stepanov, Sergey, Sanishvili, Ruslan, Becker, Michael, Winter, Graeme, Sauter, Nicholas K., Smith, Janet L., and Fischetti, Robert F. Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system. United States: N. p., 2014.
Web. doi:10.1107/S1600576714022730.
Pothineni, Sudhir Babu, Venugopalan, Nagarajan, Ogata, Craig M., Hilgart, Mark C., Stepanov, Sergey, Sanishvili, Ruslan, Becker, Michael, Winter, Graeme, Sauter, Nicholas K., Smith, Janet L., & Fischetti, Robert F. Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system. United States. https://doi.org/10.1107/S1600576714022730
Pothineni, Sudhir Babu, Venugopalan, Nagarajan, Ogata, Craig M., Hilgart, Mark C., Stepanov, Sergey, Sanishvili, Ruslan, Becker, Michael, Winter, Graeme, Sauter, Nicholas K., Smith, Janet L., and Fischetti, Robert F. Tue .
"Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system". United States. https://doi.org/10.1107/S1600576714022730. https://www.osti.gov/servlets/purl/1212769.
@article{osti_1212769,
title = {Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system},
author = {Pothineni, Sudhir Babu and Venugopalan, Nagarajan and Ogata, Craig M. and Hilgart, Mark C. and Stepanov, Sergey and Sanishvili, Ruslan and Becker, Michael and Winter, Graeme and Sauter, Nicholas K. and Smith, Janet L. and Fischetti, Robert F.},
abstractNote = {The calculation of single- and multi-crystal data collection strategies and a data processing pipeline have been tightly integrated into the macromolecular crystallographic data acquisition and beamline control software JBluIce. Both tasks employ wrapper scripts around existing crystallographic software. JBluIce executes scripts through a distributed resource management system to make efficient use of all available computing resources through parallel processing. The JBluIce single-crystal data collection strategy feature uses a choice of strategy programs to help users rank sample crystals and collect data. The strategy results can be conveniently exported to a data collection run. The JBluIce multi-crystal strategy feature calculates a collection strategy to optimize coverage of reciprocal space in cases where incomplete data are available from previous samples. The JBluIce data processing runs simultaneously with data collection using a choice of data reduction wrappers for integration and scaling of newly collected data, with an option for merging with pre-existing data. Data are processed separately if collected from multiple sites on a crystal or from multiple crystals, then scaled and merged. Results from all strategy and processing calculations are displayed in relevant tabs of JBluIce.},
doi = {10.1107/S1600576714022730},
journal = {Journal of Applied Crystallography (Online)},
number = 6,
volume = 47,
place = {United States},
year = {Tue Nov 18 00:00:00 EST 2014},
month = {Tue Nov 18 00:00:00 EST 2014}
}
Web of Science
Works referenced in this record:
Linking Crystallographic Model and Data Quality
journal, May 2012
- Karplus, P. A.; Diederichs, K.
- Science, Vol. 336, Issue 6084
EPICS controlled sample mounting robots at the GM/CA CAT
journal, November 2007
- Makarov, O. A.; Benn, R.; Corcoran, S.
- Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 582, Issue 1
Micro-crystallography comes of age
journal, October 2012
- Smith, Janet L.; Fischetti, Robert F.; Yamamoto, Masaki
- Current Opinion in Structural Biology, Vol. 22, Issue 5
Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE
journal, February 2009
- Paithankar, Karthik S.; Owen, Robin Leslie; Garman, Elspeth F.
- Journal of Synchrotron Radiation, Vol. 16, Issue 2
Micro-Crystallography Developments at GM∕CA-CAT at the APS
conference, January 2010
- Xu, Shenglan; Makarov, Oleg; Benn, Rich
- AIP Conference Proceedings, Vol. 1234, Issue 1, Article No. 905
High-Resolution Crystal Structure of an Engineered Human 2-Adrenergic G Protein-Coupled Receptor
journal, October 2007
- Cherezov, V.; Rosenbaum, D. M.; Hanson, M. A.
- Science, Vol. 318, Issue 5854
Automated data collection for macromolecular crystallography
journal, September 2011
- Winter, Graeme; McAuley, Katherine E.
- Methods, Vol. 55, Issue 1
Crystal structure of the β2 adrenergic receptor–Gs protein complex
journal, July 2011
- Rasmussen, Søren G. F.; DeVree, Brian T.; Zou, Yaozhong
- Nature, Vol. 477, Issue 7366
Control system for the 2nd generation Berkeley automounters (BAM2) at GM/CA-CAT macromolecular crystallography beamlines
journal, September 2011
- Makarov, O.; Hilgart, M.; Ogata, C.
- Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 649, Issue 1
Mini-beam collimator enables microcrystallography experiments on standard beamlines
journal, January 2009
- Fischetti, Robert F.; Xu, Shenglan; Yoder, Derek W.
- Journal of Synchrotron Radiation, Vol. 16, Issue 2
Flavivirus NS1 Structures Reveal Surfaces for Associations with Membranes and the Immune System
journal, February 2014
- Akey, D. L.; Brown, W. C.; Dutta, S.
- Science, Vol. 343, Issue 6173
Experimental determination of the radiation dose limit for cryocooled protein crystals
journal, March 2006
- Owen, R. L.; Rudino-Pinera, E.; Garman, E. F.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 13
STRATEGY : a program to optimize the starting spindle angle and scan range for X-ray data collection
journal, October 1997
- Ravelli, R. B. G.; Sweet, R. M.; Skinner, J. M.
- Journal of Applied Crystallography, Vol. 30, Issue 5
The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments
journal, June 2013
- Brockhauser, Sandor; Ravelli, Raimond B. G.; McCarthy, Andrew A.
- Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
The CCP4 suite programs for protein crystallography
journal, September 1994
- ,
- Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 5, p. 760-763
Better models by discarding data?
journal, June 2013
- Diederichs, K.; Karplus, P. A.
- Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
Scaling and assessment of data quality
journal, December 2005
- Evans, Philip
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82
An introduction to data reduction: space-group determination, scaling and intensity statistics
journal, March 2011
- Evans, Philip R.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
On the treatment of negative intensity observations
journal, July 1978
- French, S.; Wilson, K.
- Acta Crystallographica Section A, Vol. 34, Issue 4
MxCuBE : a synchrotron beamline control environment customized for macromolecular crystallography experiments
journal, July 2010
- Gabadinho, José; Beteva, Antonia; Guijarro, Matias
- Journal of Synchrotron Radiation, Vol. 17, Issue 5
Web-Ice : integrated data collection and analysis for macromolecular crystallography
journal, January 2008
- González, A.; Moorhead, P.; McPhillips, S. E.
- Journal of Applied Crystallography, Vol. 41, Issue 1
Automated sample-scanning methods for radiation damage mitigation and diffraction-based centering of macromolecular crystals
journal, July 2011
- Hilgart, Mark C.; Sanishvili, Ruslan; Ogata, Craig M.
- Journal of Synchrotron Radiation, Vol. 18, Issue 5
EDNA : a framework for plugin-based applications applied to X-ray experiment online data analysis
journal, October 2009
- Incardona, Marie-Françoise; Bourenkov, Gleb P.; Levik, Karl
- Journal of Synchrotron Radiation, Vol. 16, Issue 6
XDS
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
Integration of macromolecular diffraction data
journal, October 1999
- Leslie, A. G. W.
- Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 10
Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data
journal, June 2013
- Liu, Qun; Liu, Qinglian; Hendrickson, Wayne A.
- Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
Blu-Ice and the Distributed Control System : software for data acquisition and instrument control at macromolecular crystallography beamlines
journal, November 2002
- McPhillips, Timothy M.; McPhillips, Scott E.; Chiu, Hsiu-Ju
- Journal of Synchrotron Radiation, Vol. 9, Issue 6
Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF
journal, May 2013
- Monaco, Stéphanie; Gordon, Elspeth; Bowler, Matthew W.
- Journal of Applied Crystallography, Vol. 46, Issue 3
Choice of data-collection parameters based on statistic modelling
journal, June 2003
- Popov, Alexander N.; Bourenkov, Gleb P.
- Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 7
Automated detection and centring of cryocooled protein crystals
journal, October 2006
- Pothineni, Sudhir Babu; Strutz, Tilo; Lamzin, Victor S.
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 11
Robust indexing for automatic data collection
journal, May 2004
- Sauter, Nicholas K.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 37, Issue 3
Autoindexing the diffraction patterns from crystals with a pseudotranslation
journal, May 2009
- Sauter, Nicholas K.; Zwart, Peter H.
- Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 6
JBluIce–EPICS control system for macromolecular crystallography
journal, February 2011
- Stepanov, Sergey; Makarov, Oleg; Hilgart, Mark
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 3
AutoDrug : fully automated macromolecular crystallography workflows for fragment-based drug discovery
journal, April 2013
- Tsai, Yingssu; McPhillips, Scott E.; González, Ana
- Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 5
Data processing and analysis with the autoPROC toolbox
journal, March 2011
- Vonrhein, Clemens; Flensburg, Claus; Keller, Peter
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Global indicators of X-ray data quality
journal, April 2001
- Weiss, Manfred S.
- Journal of Applied Crystallography, Vol. 34, Issue 2
xia2 : an expert system for macromolecular crystallography data reduction
journal, December 2009
- Winter, G.
- Journal of Applied Crystallography, Vol. 43, Issue 1
Integration of macromolecular diffraction data
book, April 2012
- Leslie, A. G. W.
- International Tables for Crystallography
Integration of macromolecular diffraction data
book, October 2006
- Leslie, A. G. W.
- International Tables for Crystallography
Works referencing / citing this record:
Crystal structure of human PLD1 provides insight into activation by PI(4,5)P2 and RhoA
journal, March 2020
- Bowling, Forrest Z.; Salazar, Christian M.; Bell, Justin A.
- Nature Chemical Biology, Vol. 16, Issue 4
In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures
journal, January 2016
- Huang, Chia-Ying; Olieric, Vincent; Ma, Pikyee
- Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 1
DA+ data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines
journal, January 2018
- Wojdyla, Justyna Aleksandra; Kaminski, Jakub W.; Panepucci, Ezequiel
- Journal of Synchrotron Radiation, Vol. 25, Issue 1
High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions
journal, January 2018
- Broecker, Jana; Morizumi, Takefumi; Ou, Wei-Lin
- Nature Protocols, Vol. 13, Issue 2