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:
- 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.
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
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.
@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}
}
https://doi.org/10.1107/S160057671901673X
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
Macromolecular microcrystallography
journal, April 2011
- Evans, Gwyndaf; Axford, Danny; Waterman, David
- Crystallography Reviews, Vol. 17, Issue 2
High-speed raster-scanning synchrotron serial microcrystallography with a high-precision piezo-scanner
journal, August 2018
- Gao, Yuan; Xu, Weihe; Shi, Wuxian
- Journal of Synchrotron Radiation, Vol. 25, Issue 5
Structures from Anomalous Diffraction of Native Biological Macromolecules
journal, May 2012
- Liu, Q.; Dahmane, T.; Zhang, Z.
- Science, Vol. 336, Issue 6084
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
X-ray radiation damage to biological macromolecules: further insights
journal, January 2017
- Garman, Elspeth F.; Weik, Martin
- Journal of Synchrotron Radiation, Vol. 24, Issue 1
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
Serial crystallography on in vivo grown microcrystals using synchrotron radiation
journal, February 2014
- Gati, Cornelius; Bourenkov, Gleb; Klinge, Marco
- IUCrJ, Vol. 1, Issue 2
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
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
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
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
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
In situ serial crystallography for rapid de novo membrane protein structure determination
journal, August 2018
- Huang, Chia-Ying; Olieric, Vincent; Howe, Nicole
- Communications Biology, Vol. 1, Issue 1
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
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
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
Sample manipulation and data assembly for robust microcrystal synchrotron crystallography
journal, April 2018
- Guo, Gongrui; Fuchs, Martin R.; Shi, Wuxian
- IUCrJ, Vol. 5, Issue 3
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
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
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
Serial femtosecond crystallography: the first five years
journal, February 2015
- Schlichting, Ilme
- IUCrJ, Vol. 2, Issue 2, p. 246-255
Sulfur-SAD phasing from microcrystals utilizing low-energy X-rays
journal, June 2019
- Dauter, Zbigniew
- IUCrJ, Vol. 6, Issue 4
Synchrotron microcrystal native-SAD phasing at a low energy
journal, May 2019
- Guo, Gongrui; Zhu, Ping; Fuchs, Martin R.
- IUCrJ, Vol. 6, Issue 4
Long-wavelength native-SAD phasing: opportunities and challenges
journal, April 2019
- Basu, Shibom; Olieric, Vincent; Leonarski, Filip
- IUCrJ, Vol. 6, Issue 3
Protein microcrystallography using synchrotron radiation
journal, August 2017
- Yamamoto, Masaki; Hirata, Kunio; Yamashita, Keitaro
- IUCrJ, Vol. 4, Issue 5
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
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
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
XFELs for structure and dynamics in biology
journal, May 2017
- Spence, J. C. H.
- IUCrJ, Vol. 4, Issue 4