Best practices for high data-rate macromolecular crystallography (HDRMX)

In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (...

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Main Authors:	Herbert J. Bernstein, Lawrence C. Andrews, Jorge A. Diaz Jr., Jean Jakoncic, Thu Nguyen, Nicholas K. Sauter, Alexei S. Soares, Justin Y. Wei, Maciej R. Wlodek, Mario A. Xerri
Format:	Article
Language:	English
Published:	AIP Publishing LLC and ACA 2020-01-01
Series:	Structural Dynamics
Online Access:	http://dx.doi.org/10.1063/1.5128498

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spelling	doaj-f3fbf4ab34284d61b54c34b2b70c33802020-11-25T01:45:06ZengAIP Publishing LLC and ACAStructural Dynamics2329-77782020-01-0171014302014302-810.1063/1.5128498Best practices for high data-rate macromolecular crystallography (HDRMX)Herbert J. Bernstein0Lawrence C. Andrews1Jorge A. Diaz Jr.2Jean Jakoncic3Thu Nguyen4Nicholas K. Sauter5Alexei S. Soares6Justin Y. Wei7Maciej R. Wlodek8Mario A. Xerri9 Ronin Institute for Independent Scholarship, c/o NSLS-II Bldg 745, Brookhaven National Laboratory, Upton, New York 11973, USA Ronin Institute for Independent Scholarship, 9515 NE 137th St., Kirkland, Washington 98034, USA Ronin Institute for Independent Scholarship, c/o NSLS-II Bldg 745, Brookhaven National Laboratory, Upton, New York 11973, USA Brookhaven National Laboratory, NSLS-II Bldg 745, Upton, New York 11973, USA Stony Brook University, Stony Brook, New York 11794, USA Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720, USA Brookhaven National Laboratory, NSLS-II Bldg 745, Upton, New York 11973, USA Mount Sinai High School, 110 N Country Rd., Mt Sinai, New York 11766, USA Stony Brook University, Stony Brook, New York 11794, USA Mount Sinai High School, 110 N Country Rd., Mt Sinai, New York 11766, USAIn macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations of file systems favor a transition from simple one-file-per-image systems such as CBF to image container systems such as HDF5. This further increases the load on computers and networks and requires a re-examination of the presentation of metadata. In this paper, we discuss three important components of this problem—improved approaches to the clustering of images to better support experiments on polymorphs and dynamics, recent and upcoming changes in metadata for Eiger images, and software to rapidly validate images in the revised Eiger format.http://dx.doi.org/10.1063/1.5128498
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Herbert J. Bernstein Lawrence C. Andrews Jorge A. Diaz Jr. Jean Jakoncic Thu Nguyen Nicholas K. Sauter Alexei S. Soares Justin Y. Wei Maciej R. Wlodek Mario A. Xerri
spellingShingle	Herbert J. Bernstein Lawrence C. Andrews Jorge A. Diaz Jr. Jean Jakoncic Thu Nguyen Nicholas K. Sauter Alexei S. Soares Justin Y. Wei Maciej R. Wlodek Mario A. Xerri Best practices for high data-rate macromolecular crystallography (HDRMX) Structural Dynamics
author_facet	Herbert J. Bernstein Lawrence C. Andrews Jorge A. Diaz Jr. Jean Jakoncic Thu Nguyen Nicholas K. Sauter Alexei S. Soares Justin Y. Wei Maciej R. Wlodek Mario A. Xerri
author_sort	Herbert J. Bernstein
title	Best practices for high data-rate macromolecular crystallography (HDRMX)
title_short	Best practices for high data-rate macromolecular crystallography (HDRMX)
title_full	Best practices for high data-rate macromolecular crystallography (HDRMX)
title_fullStr	Best practices for high data-rate macromolecular crystallography (HDRMX)
title_full_unstemmed	Best practices for high data-rate macromolecular crystallography (HDRMX)
title_sort	best practices for high data-rate macromolecular crystallography (hdrmx)
publisher	AIP Publishing LLC and ACA
series	Structural Dynamics
issn	2329-7778
publishDate	2020-01-01
description	In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations of file systems favor a transition from simple one-file-per-image systems such as CBF to image container systems such as HDF5. This further increases the load on computers and networks and requires a re-examination of the presentation of metadata. In this paper, we discuss three important components of this problem—improved approaches to the clustering of images to better support experiments on polymorphs and dynamics, recent and upcoming changes in metadata for Eiger images, and software to rapidly validate images in the revised Eiger format.
url	http://dx.doi.org/10.1063/1.5128498
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Best practices for high data-rate macromolecular crystallography (HDRMX)

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