Limits...
Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system.

Pothineni SB, Venugopalan N, Ogata CM, Hilgart MC, Stepanov S, Sanishvili R, Becker M, Winter G, Sauter NK, Smith JL, Fischetti RF - J Appl Crystallogr (2014)

Bottom Line: The strategy results can be conveniently exported to a data collection run.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: GM/CA@APS, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, IL 60439, USA.

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.

No MeSH data available.


Hierarchy of data collection modes in JBluIce.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4248568&req=5

fig6: Hierarchy of data collection modes in JBluIce.

Mentions: JBluIce has several data collection modes (Hilgart et al., 2011 ▶) to address the varied requirements of the challenging problems users bring to GM/CA, including membrane-protein crystals, frequently grown in lipidic cubic phase, crystals of macromolecular complexes and crystals with large unit cells, which are common with large complexes. The data collection modes are named Standard, Vector and Raster (Fig. 6 ▶). Standard mode has a Native option and an Anomalous option with a choice of single- or multi-wavelength collection. In Vector mode, an angular sweep of data can be partitioned among discrete sites along a crystal or recorded in a continuous helical geometry, with the additional option for inverse-beam geometry with true Friedel pairs collected from the same site in the crystal. Also, Vector-mode data can be collected with angular overlaps between discrete sites to help with scaling the separate sites. Raster mode is for data collection from multiple sites, no matter whether these sites are from a single crystal or from multiple crystals within a single sample loop. The different data collection modes present interesting challenges to the two data processing pipelines, fast_dp and GMCAproc.


Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system.

Pothineni SB, Venugopalan N, Ogata CM, Hilgart MC, Stepanov S, Sanishvili R, Becker M, Winter G, Sauter NK, Smith JL, Fischetti RF - J Appl Crystallogr (2014)

Hierarchy of data collection modes in JBluIce.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4248568&req=5

fig6: Hierarchy of data collection modes in JBluIce.
Mentions: JBluIce has several data collection modes (Hilgart et al., 2011 ▶) to address the varied requirements of the challenging problems users bring to GM/CA, including membrane-protein crystals, frequently grown in lipidic cubic phase, crystals of macromolecular complexes and crystals with large unit cells, which are common with large complexes. The data collection modes are named Standard, Vector and Raster (Fig. 6 ▶). Standard mode has a Native option and an Anomalous option with a choice of single- or multi-wavelength collection. In Vector mode, an angular sweep of data can be partitioned among discrete sites along a crystal or recorded in a continuous helical geometry, with the additional option for inverse-beam geometry with true Friedel pairs collected from the same site in the crystal. Also, Vector-mode data can be collected with angular overlaps between discrete sites to help with scaling the separate sites. Raster mode is for data collection from multiple sites, no matter whether these sites are from a single crystal or from multiple crystals within a single sample loop. The different data collection modes present interesting challenges to the two data processing pipelines, fast_dp and GMCAproc.

Bottom Line: The strategy results can be conveniently exported to a data collection run.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: GM/CA@APS, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, IL 60439, USA.

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.

No MeSH data available.