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

Abstract

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.

Authors:
ORCiD logo [1]; ORCiD logo [2];  [1];  [1];  [3];  [4]; ORCiD logo [1]; ORCiD logo [5];  [3];  [5]
  1. Brookhaven National Lab. (BNL), Upton, NY (United States)
  2. Ronin Inst. for Independent Scholarship, Kirkland, WA (United States)
  3. Stony Brook Univ., NY (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Mount Sinai High School, Mt Sinai, NY (United States)
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
OSTI Identifier:
1607978
Alternate Identifier(s):
OSTI ID: 1581838
Report Number(s):
BNL-213788-2020-JAAM
Journal ID: ISSN 2329-7778
Grant/Contract Number:  
SC0012704; AC02-98CH10886; P41RR012408; P41GM103473; P41GM111244; R01GM117126; P30GM133893; R21GM129570
Resource Type:
Accepted Manuscript
Journal Name:
Structural Dynamics
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2329-7778
Publisher:
American Crystallographic Association/AIP
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE

Citation Formats

Bernstein, Herbert J., Andrews, Lawrence C., Diaz, Jorge A., Jakoncic, Jean, Nguyen, Thu, Sauter, Nicholas K., Soares, Alexei S., Wei, Justin Y., Wlodek, Maciej R., and Xerri, Mario A. Best practices for high data-rate macromolecular crystallography (HDRMX). United States: N. p., 2020. Web. https://doi.org/10.1063/1.5128498.
Bernstein, Herbert J., Andrews, Lawrence C., Diaz, Jorge A., Jakoncic, Jean, Nguyen, Thu, Sauter, Nicholas K., Soares, Alexei S., Wei, Justin Y., Wlodek, Maciej R., & Xerri, Mario A. Best practices for high data-rate macromolecular crystallography (HDRMX). United States. https://doi.org/10.1063/1.5128498
Bernstein, Herbert J., Andrews, Lawrence C., Diaz, Jorge A., Jakoncic, Jean, Nguyen, Thu, Sauter, Nicholas K., Soares, Alexei S., Wei, Justin Y., Wlodek, Maciej R., and Xerri, Mario A. Thu . "Best practices for high data-rate macromolecular crystallography (HDRMX)". United States. https://doi.org/10.1063/1.5128498. https://www.osti.gov/servlets/purl/1607978.
@article{osti_1607978,
title = {Best practices for high data-rate macromolecular crystallography (HDRMX)},
author = {Bernstein, Herbert J. and Andrews, Lawrence C. and Diaz, Jorge A. and Jakoncic, Jean and Nguyen, Thu and Sauter, Nicholas K. and Soares, Alexei S. and Wei, Justin Y. and Wlodek, Maciej R. and Xerri, Mario A.},
abstractNote = {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.},
doi = {10.1063/1.5128498},
journal = {Structural Dynamics},
number = 1,
volume = 7,
place = {United States},
year = {2020},
month = {1}
}

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