Tools for supporting solution scattering during the COVID-19 pandemic

Yang, Lin; Lazo, Edwin; Byrnes, James; Chodankar, Shirish; Antonelli, Stephen; Rakitin, Maksim

doi:10.1107/S160057752100521X

Title: Tools for supporting solution scattering during the COVID-19 pandemic

Abstract

During the COVID-19 pandemic, synchrotron beamlines were forced to limit user access. Performing routine measurements became a challenge. At the Life Science X-ray Scattering (LiX) beamline, new instrumentation and mail-in protocols have been developed to remove the access barrier to solution scattering measurements. Our efforts took advantage of existing instrumentation and coincided with the larger effort at NSLS-II to support remote measurements. Given the limited staff–user interaction for mail-in measurements, additional software tools have been developed to ensure data quality, to automate the adjustments in data processing, as users would otherwise rely on the experience of the beamline staff, and produce a summary of the initial assessments of the data. This report describes the details of these developments.

Authors:

;

; Antonelli, Stephen;

Publication Date:: Fri Jun 25 00:00:00 EDT 2021

Research Org.:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1798531

Alternate Identifier(s):: OSTI ID: 1811459

Report Number(s):: BNL-221930-2021-JAAM
Journal ID: ISSN 1600-5775; JSYRES; PII: S160057752100521X

Grant/Contract Number:: KP1605010; SC0012704; P30GM133893; S10OD012331

Resource Type:: Published Article

Journal Name:: Journal of Synchrotron Radiation (Online)

Additional Journal Information:: Journal Name: Journal of Synchrotron Radiation (Online) Journal Volume: 28 Journal Issue: 4; Journal ID: ISSN 1600-5775

Publisher:: International Union of Crystallography (IUCr)

Country of Publication:: Denmark

Language:: English

Subject:: 99 GENERAL AND MISCELLANEOUS; mail-in; solution scattering; automation

Citation Formats


                    Yang, Lin, Lazo, Edwin, Byrnes, James, Chodankar, Shirish, Antonelli, Stephen, and Rakitin, Maksim. Tools for supporting solution scattering during the COVID-19 pandemic.  Denmark: N. p., 2021. 
Web.  doi:10.1107/S160057752100521X.

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                    Yang, Lin, Lazo, Edwin, Byrnes, James, Chodankar, Shirish, Antonelli, Stephen, & Rakitin, Maksim. Tools for supporting solution scattering during the COVID-19 pandemic.  Denmark.  https://doi.org/10.1107/S160057752100521X

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                    Yang, Lin, Lazo, Edwin, Byrnes, James, Chodankar, Shirish, Antonelli, Stephen, and Rakitin, Maksim. Fri .  
"Tools for supporting solution scattering during the COVID-19 pandemic".  Denmark.  https://doi.org/10.1107/S160057752100521X.

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@article{osti_1798531,

  title        = {Tools for supporting solution scattering during the COVID-19 pandemic},

  author       = {Yang, Lin and Lazo, Edwin and Byrnes, James and Chodankar, Shirish and Antonelli, Stephen and Rakitin, Maksim},

  abstractNote = {During the COVID-19 pandemic, synchrotron beamlines were forced to limit user access. Performing routine measurements became a challenge. At the Life Science X-ray Scattering (LiX) beamline, new instrumentation and mail-in protocols have been developed to remove the access barrier to solution scattering measurements. Our efforts took advantage of existing instrumentation and coincided with the larger effort at NSLS-II to support remote measurements. Given the limited staff–user interaction for mail-in measurements, additional software tools have been developed to ensure data quality, to automate the adjustments in data processing, as users would otherwise rely on the experience of the beamline staff, and produce a summary of the initial assessments of the data. This report describes the details of these developments.},

  doi          = {10.1107/S160057752100521X},

  journal      = {Journal of Synchrotron Radiation (Online)},

  number       = 4,

  volume       = 28,

  place        = {Denmark},

  year         = {Fri Jun 25 00:00:00 EDT 2021},

  month        = {Fri Jun 25 00:00:00 EDT 2021}

}

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Works referenced in this record:

BioSAXS Sample Changer: a robotic sample changer for rapid and reliable high-throughput X-ray solution scattering experiments
journal, January 2015

Round, Adam; Felisaz, Franck; Fodinger, Lukas
Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 1
DOI: 10.1107/S1399004714026959

Ab initio electron density determination directly from solution scattering data
journal, January 2018

Grant, Thomas D.
Nature Methods, Vol. 15, Issue 3
DOI: 10.1038/nmeth.4581

New tools for calibrating diffraction setups
journal, February 2020

Kieffer, J.; Valls, V.; Blanc, N.
Journal of Synchrotron Radiation, Vol. 27, Issue 2
DOI: 10.1107/S1600577520000776

Mail-in crystallography program at Brookhaven National Laboratory's National Synchrotron Light Source
journal, October 2006

Robinson, Howard; Soares, Alexei S.; Becker, Michael
Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 11
DOI: 10.1107/S0907444906026321

Solution scattering at the Life Science X-ray Scattering (LiX) beamline
journal, March 2020

Yang, Lin; Antonelli, Stephen; Chodankar, Shirish
Journal of Synchrotron Radiation, Vol. 27, Issue 3
DOI: 10.1107/S1600577520002362

High-Throughput SAXS for the Characterization of Biomolecules in Solution: A Practical Approach
book, October 2013

Dyer, Kevin N.; Hammel, Michal; Rambo, Robert P.
Structural Genomics
DOI: 10.1007/978-1-62703-691-7_18

The Longest Run of Heads
journal, May 1990

Schilling, Mark F.
The College Mathematics Journal, Vol. 21, Issue 3
DOI: 10.1080/07468342.1990.11973306

Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra
journal, April 2015

Franke, Daniel; Jeffries, Cy M.; Svergun, Dmitri I.
Nature Methods, Vol. 12, Issue 5
DOI: 10.1038/nmeth.3358

ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions
journal, June 2017

Franke, D.; Petoukhov, M. V.; Konarev, P. V.
Journal of Applied Crystallography, Vol. 50, Issue 4
DOI: 10.1107/S1600576717007786

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
journal, July 2009

Hura, Greg L.; Menon, Angeli L.; Hammel, Michal
Nature Methods, Vol. 6, Issue 8
DOI: 10.1038/nmeth.1353

Mail-in data collection at SPring-8 protein crystallography beamlines
journal, April 2008

Okazaki, Nobuo; Hasegawa, Kazuya; Ueno, Go
Journal of Synchrotron Radiation, Vol. 15, Issue 3
DOI: 10.1107/S0909049507064679

Development of tools to automate quantitative analysis of radiation damage in SAXS experiments
journal, January 2017

Brooks-Bartlett, Jonathan C.; Batters, Rebecca A.; Bury, Charles S.
Journal of Synchrotron Radiation, Vol. 24, Issue 1
DOI: 10.1107/S1600577516015083

High-throughput biological small-angle X-ray scattering with a robotically loaded capillary cell
journal, February 2012

Nielsen, S. S.; Møller, M.; Gillilan, R. E.
Journal of Applied Crystallography, Vol. 45, Issue 2
DOI: 10.1107/S0021889812000957

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Similar Records

Title: Tools for supporting solution scattering during the COVID-19 pandemic

Abstract

Citation Formats

BioSAXS Sample Changer: a robotic sample changer for rapid and reliable high-throughput X-ray solution scattering experiments journal, January 2015

Ab initio electron density determination directly from solution scattering data journal, January 2018

New tools for calibrating diffraction setups journal, February 2020

Mail-in crystallography program at Brookhaven National Laboratory's National Synchrotron Light Source journal, October 2006

Solution scattering at the Life Science X-ray Scattering (LiX) beamline journal, March 2020

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The Longest Run of Heads journal, May 1990

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Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS) journal, July 2009

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High-throughput biological small-angle X-ray scattering with a robotically loaded capillary cell journal, February 2012

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journal, January 2015

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journal, January 2018

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journal, February 2020

Mail-in crystallography program at Brookhaven National Laboratory's National Synchrotron Light Source
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journal, April 2015

ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions
journal, June 2017

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
journal, July 2009

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