Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: PyMDA : microcrystal data assembly using Python

Abstract

The recent developments at microdiffraction X-ray beamlines are making microcrystals of macromolecules appealing subjects for routine structural analysis. Microcrystal diffraction data collected at synchrotron microdiffraction beamlines may be radiation-damaged with incomplete data per microcrystal and with unit cell variations. We have previously devised a multi-stage data assembly method for microcrystal synchrotron crystallography. Here we have implemented the strategy as a Python program for microcrystal data assembly (PyMDA). PyMDA optimizes microcrystal data quality including weak anomalous signals through iterative crystal and frame rejections. Beyond microcrystals, PyMDA may be applicable for assembling data sets from larger crystals for improved data quality.

Authors:
; ; ; ; ORCiD logo; ORCiD logo
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program; National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Workforce Development for Teachers and Scientists (WDTS)
OSTI Identifier:
1617953
Alternate Identifier(s):
OSTI ID: 1579902; OSTI ID: 1777433
Report Number(s):
BNL-212432-2019-JAAM; BNL-221258-2021-JAAM
Journal ID: ISSN 1600-5767; JACGAR; PII: S160057671901673X
Grant/Contract Number:  
SC0012704; GM107462; P30GM133893; KP1607010
Resource Type:
Published Article
Journal Name:
Journal of Applied Crystallography (Online)
Additional Journal Information:
Journal Name: Journal of Applied Crystallography (Online) Journal Volume: 53 Journal Issue: 1; Journal ID: ISSN 1600-5767
Publisher:
International Union of Crystallography (IUCr)
Country of Publication:
Denmark
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; X-ray crystallography; microcrystal; data assembly; radiation damage; multi-crystal; python; 36 MATERIALS SCIENCE; microcrystals

Citation Formats

Takemaru, Lina, Guo, Gongrui, Zhu, Ping, Hendrickson, Wayne A., McSweeney, Sean, and Liu, Qun. PyMDA : microcrystal data assembly using Python. Denmark: N. p., 2020. Web. doi:10.1107/S160057671901673X.
Copy to clipboard
Takemaru, Lina, Guo, Gongrui, Zhu, Ping, Hendrickson, Wayne A., McSweeney, Sean, & Liu, Qun. PyMDA : microcrystal data assembly using Python. Denmark. https://doi.org/10.1107/S160057671901673X
Copy to clipboard
Takemaru, Lina, Guo, Gongrui, Zhu, Ping, Hendrickson, Wayne A., McSweeney, Sean, and Liu, Qun. Sat . "PyMDA : microcrystal data assembly using Python". Denmark. https://doi.org/10.1107/S160057671901673X.
Copy to clipboard
@article{osti_1617953,
title = {PyMDA : microcrystal data assembly using Python},
author = {Takemaru, Lina and Guo, Gongrui and Zhu, Ping and Hendrickson, Wayne A. and McSweeney, Sean and Liu, Qun},
abstractNote = {The recent developments at microdiffraction X-ray beamlines are making microcrystals of macromolecules appealing subjects for routine structural analysis. Microcrystal diffraction data collected at synchrotron microdiffraction beamlines may be radiation-damaged with incomplete data per microcrystal and with unit cell variations. We have previously devised a multi-stage data assembly method for microcrystal synchrotron crystallography. Here we have implemented the strategy as a Python program for microcrystal data assembly (PyMDA). PyMDA optimizes microcrystal data quality including weak anomalous signals through iterative crystal and frame rejections. Beyond microcrystals, PyMDA may be applicable for assembling data sets from larger crystals for improved data quality.},
doi = {10.1107/S160057671901673X},
journal = {Journal of Applied Crystallography (Online)},
number = 1,
volume = 53,
place = {Denmark},
year = {2020},
month = {2}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1107/S160057671901673X
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Diffraction-geometry refinement in the DIALS framework
journal, March 2016

  • Waterman, David G.; Winter, Graeme; Gildea, Richard J.
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 4
  • DOI: 10.1107/S2059798316002187

Macromolecular microcrystallography
journal, April 2011

High-speed raster-scanning synchrotron serial microcrystallography with a high-precision piezo-scanner
journal, August 2018

Structures from Anomalous Diffraction of Native Biological Macromolecules
journal, May 2012

Low-dose fixed-target serial synchrotron crystallography
journal, March 2017

  • Owen, Robin L.; Axford, Danny; Sherrell, Darren A.
  • Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 4, p. 373-378
  • DOI: 10.1107/S2059798317002996

X-ray radiation damage to biological macromolecules: further insights
journal, January 2017

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
  • DOI: 10.1016/j.sbi.2012.09.001

Serial crystallography on in vivo grown microcrystals using synchrotron radiation
journal, February 2014

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography
journal, July 2013

  • Foadi, James; Aller, Pierre; Alguel, Yilmaz
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 8
  • DOI: 10.1107/S0907444913012274

MeshAndCollect : an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines
journal, October 2015

  • Zander, Ulrich; Bourenkov, Gleb; Popov, Alexander N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 11
  • DOI: 10.1107/S1399004715017927

EIGER detector: application in macromolecular crystallography
journal, August 2016

  • Casanas, Arnau; Warshamanage, Rangana; Finke, Aaron D.
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 9
  • DOI: 10.1107/S2059798316012304

Direct measurement of X-ray-induced heating of microcrystals
journal, May 2019

  • Warren, Anna J.; Axford, Danny; Owen, Robin L.
  • Journal of Synchrotron Radiation, Vol. 26, Issue 4
  • DOI: 10.1107/S1600577519003849

In situ serial crystallography for rapid de novo membrane protein structure determination
journal, August 2018

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
  • DOI: 10.1107/S0907444913001479

DIALS : implementation and evaluation of a new integration package
journal, February 2018

  • Winter, Graeme; Waterman, David G.; Parkhurst, James M.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 2
  • DOI: 10.1107/S2059798317017235

The ID23-2 structural biology microfocus beamline at the ESRF
journal, December 2009

  • Flot, David; Mairs, Trevor; Giraud, Thierry
  • Journal of Synchrotron Radiation, Vol. 17, Issue 1
  • DOI: 10.1107/S0909049509041168

Sample manipulation and data assembly for robust microcrystal synchrotron crystallography
journal, April 2018

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
journal, April 2015

  • Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 5
  • DOI: 10.1107/S1399004715004514

Predicting the X-ray lifetime of protein crystals
journal, December 2013

  • Zeldin, O. B.; Brockhauser, S.; Bremridge, J.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 51
  • DOI: 10.1073/pnas.1315879110

How good are my data and what is the resolution?
journal, June 2013

  • Evans, Philip R.; Murshudov, Garib N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913000061

Serial femtosecond crystallography: the first five years
journal, February 2015

Sulfur-SAD phasing from microcrystals utilizing low-energy X-rays
journal, June 2019

Synchrotron microcrystal native-SAD phasing at a low energy
journal, May 2019

Long-wavelength native-SAD phasing: opportunities and challenges
journal, April 2019

Protein microcrystallography using synchrotron radiation
journal, August 2017

KAMO : towards automated data processing for microcrystals
journal, April 2018

  • Yamashita, Keitaro; Hirata, Kunio; Yamamoto, Masaki
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 5
  • DOI: 10.1107/S2059798318004576

Long-wavelength Mesh&Collect native SAD phasing from microcrystals
journal, February 2019

  • Cianci, Michele; Nanao, Max; Schneider, Thomas R.
  • Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 2
  • DOI: 10.1107/S2059798319002031

The minimum crystal size needed for a complete diffraction data set
journal, March 2010

  • Holton, James M.; Frankel, Kenneth A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007262

XFELs for structure and dynamics in biology
journal, May 2017

    Sort by:
    [ × clear filter / sort ]

    Similar Records in DOE PAGES and OSTI.GOV collections: