Open Access

Journal of Applied Crystallography, volume 40, issue 4, pages 658-674

Phasercrystallographic software

McCoy Airlie J. ¹

Grosse-Kunstleve Ralf W. ²

Adams Paul D. ²

Winn Martyn D. ³

Storoni Laurent C. ¹

Read Randy J. ¹

Hide authors affiliations Show authors affiliations: 3 affiliations

Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK |

Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720-8118, USA |

Daresbury Laboratory, Warrington WA4 4AD, UK |

Publication type: Journal Article

Publication date: 2007-07-13

International Union of Crystallography (IUCr)

Journal: Journal of Applied Crystallography

Quartile SCImago

Quartile WOS

Impact factor: 6.1

ISSN: 00218898, 16005767

DOI: 10.1107/S0021889807021206

Copy DOI

PubMed ID: 19461840

General Biochemistry, Genetics and Molecular Biology

Abstract

Phaseris a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented inPhaserhave been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations betweenF⁺andF⁻, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use meanFand anomalous differences ΔF. One of the design concepts ofPhaserwas that it be capable of a high degree of automation. To this end,Phaser(written in C++) can be called directly from Python, although it can also be called using traditionalCCP4keyword-style input.Phaseris a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

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Citations by journals

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Journal of Biological Chemistry	Journal of Biological Chemistry, 1234, 7.22% Journal of Biological Chemistry 1234 publications, 7.22%
Nature Communications	Nature Communications, 968, 5.67% Nature Communications 968 publications, 5.67%
Biochemistry	Biochemistry, 534, 3.13% Biochemistry 534 publications, 3.13%
Structure	Structure, 524, 3.07% Structure 524 publications, 3.07%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 508, 2.97% Proceedings of the National Academy of Sciences of the United States of America 508 publications, 2.97%
Scientific Reports	Scientific Reports, 480, 2.81% Scientific Reports 480 publications, 2.81%
Journal of Molecular Biology	Journal of Molecular Biology, 474, 2.78% Journal of Molecular Biology 474 publications, 2.78%
Acta Crystallographica Section F:Structural Biology Communications	Acta Crystallographica Section F:Structural Biology Communications, 453, 2.65% Acta Crystallographica Section F:Structural Biology Communications 453 publications, 2.65%
Journal of Medicinal Chemistry	Journal of Medicinal Chemistry, 440, 2.58% Journal of Medicinal Chemistry 440 publications, 2.58%
Nucleic Acids Research	Nucleic Acids Research, 431, 2.52% Nucleic Acids Research 431 publications, 2.52%
Nature	Nature, 405, 2.37% Nature 405 publications, 2.37%
PLoS ONE	PLoS ONE, 397, 2.32% PLoS ONE 397 publications, 2.32%
Acta Crystallographica Section D Biological Crystallography	Acta Crystallographica Section D Biological Crystallography, 356, 2.08% Acta Crystallographica Section D Biological Crystallography 356 publications, 2.08%
Acta Crystallographica Section D: Structural Biology	Acta Crystallographica Section D: Structural Biology, 315, 1.84% Acta Crystallographica Section D: Structural Biology 315 publications, 1.84%
Protein Science	Protein Science, 277, 1.62% Protein Science 277 publications, 1.62%
Biochemical and Biophysical Research Communications	Biochemical and Biophysical Research Communications, 258, 1.51% Biochemical and Biophysical Research Communications 258 publications, 1.51%
Nature Structural and Molecular Biology	Nature Structural and Molecular Biology, 255, 1.49% Nature Structural and Molecular Biology 255 publications, 1.49%
eLife	eLife, 253, 1.48% eLife 253 publications, 1.48%
FEBS Journal	FEBS Journal, 250, 1.46% FEBS Journal 250 publications, 1.46%
Acta Crystallographica Section F Structural Biology and Crystallization Communications	Acta Crystallographica Section F Structural Biology and Crystallization Communications, 250, 1.46% Acta Crystallographica Section F Structural Biology and Crystallization Communications 250 publications, 1.46%
Science	Science, 218, 1.28% Science 218 publications, 1.28%
Journal of Structural Biology	Journal of Structural Biology, 210, 1.23% Journal of Structural Biology 210 publications, 1.23%
Nature Chemical Biology	Nature Chemical Biology, 196, 1.15% Nature Chemical Biology 196 publications, 1.15%
Biochemical Journal	Biochemical Journal, 171, 1% Biochemical Journal 171 publications, 1%
Proteins: Structure, Function and Genetics	Proteins: Structure, Function and Genetics, 163, 0.95% Proteins: Structure, Function and Genetics 163 publications, 0.95%
PLoS Pathogens	PLoS Pathogens, 157, 0.92% PLoS Pathogens 157 publications, 0.92%
Cell	Cell, 156, 0.91% Cell 156 publications, 0.91%
Journal of Virology	Journal of Virology, 151, 0.88% Journal of Virology 151 publications, 0.88%
ACS Chemical Biology	ACS Chemical Biology, 137, 0.8% ACS Chemical Biology 137 publications, 0.8%
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Citations by publishers

	500 1000 1500 2000 2500 3000 3500
Springer Nature	Springer Nature, 3025, 17.71% Springer Nature 3025 publications, 17.71%
Elsevier	Elsevier, 2916, 17.07% Elsevier 2916 publications, 17.07%
American Chemical Society (ACS)	American Chemical Society (ACS), 1543, 9.03% American Chemical Society (ACS) 1543 publications, 9.03%
International Union of Crystallography (IUCr)	International Union of Crystallography (IUCr), 1493, 8.74% International Union of Crystallography (IUCr) 1493 publications, 8.74%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 1249, 7.31% American Society for Biochemistry and Molecular Biology 1249 publications, 7.31%
Wiley	Wiley, 1241, 7.27% Wiley 1241 publications, 7.27%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 613, 3.59% Public Library of Science (PLoS) 613 publications, 3.59%
Oxford University Press	Oxford University Press, 539, 3.16% Oxford University Press 539 publications, 3.16%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 508, 2.97% Proceedings of the National Academy of Sciences (PNAS) 508 publications, 2.97%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 387, 2.27% American Association for the Advancement of Science (AAAS) 387 publications, 2.27%
American Society for Microbiology	American Society for Microbiology, 376, 2.2% American Society for Microbiology 376 publications, 2.2%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 320, 1.87% Multidisciplinary Digital Publishing Institute (MDPI) 320 publications, 1.87%
eLife Sciences Publications	eLife Sciences Publications, 253, 1.48% eLife Sciences Publications 253 publications, 1.48%
Portland Press	Portland Press, 173, 1.01% Portland Press 173 publications, 1.01%
EMBO press	EMBO press, 144, 0.84% EMBO press 144 publications, 0.84%
Frontiers Media S.A.	Frontiers Media S.A., 139, 0.81% Frontiers Media S.A. 139 publications, 0.81%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 121, 0.71% Royal Society of Chemistry (RSC) 121 publications, 0.71%
Taylor & Francis	Taylor & Francis, 94, 0.55% Taylor & Francis 94 publications, 0.55%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 75, 0.44% Cold Spring Harbor Laboratory 75 publications, 0.44%
Rockefeller University Press	Rockefeller University Press, 69, 0.4% Rockefeller University Press 69 publications, 0.4%
The American Association of Immunologists	The American Association of Immunologists, 43, 0.25% The American Association of Immunologists 43 publications, 0.25%
American Society for Pharmacology and Experimental Therapeutics	American Society for Pharmacology and Experimental Therapeutics, 35, 0.2% American Society for Pharmacology and Experimental Therapeutics 35 publications, 0.2%
Federation of American Societies for Experimental Biology (FASEB)	Federation of American Societies for Experimental Biology (FASEB), 32, 0.19% Federation of American Societies for Experimental Biology (FASEB) 32 publications, 0.19%
The Royal Society	The Royal Society, 32, 0.19% The Royal Society 32 publications, 0.19%
Pleiades Publishing	Pleiades Publishing, 25, 0.15% Pleiades Publishing 25 publications, 0.15%
Biophysical Society	Biophysical Society, 25, 0.15% Biophysical Society 25 publications, 0.15%
American Association for Cancer Research (AACR)	American Association for Cancer Research (AACR), 25, 0.15% American Association for Cancer Research (AACR) 25 publications, 0.15%
American Society for Clinical Investigation	American Society for Clinical Investigation, 15, 0.09% American Society for Clinical Investigation 15 publications, 0.09%
Social Science Electronic Publishing	Social Science Electronic Publishing, 14, 0.08% Social Science Electronic Publishing 14 publications, 0.08%
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McCoy A. J. et al. Phasercrystallographic software // Journal of Applied Crystallography. 2007. Vol. 40. No. 4. pp. 658-674.

GOST all authors (up to 50) Copy

McCoy A. J., Grosse-Kunstleve R. W., Adams P. D., Winn M., Storoni L. C., Read R. J. Phasercrystallographic software // Journal of Applied Crystallography. 2007. Vol. 40. No. 4. pp. 658-674.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1107/S0021889807021206

UR - https://doi.org/10.1107%2FS0021889807021206

TI - Phasercrystallographic software

T2 - Journal of Applied Crystallography

AU - McCoy, Airlie J.

AU - Grosse-Kunstleve, Ralf W.

AU - Adams, Paul D.

AU - Winn, Martyn D.

AU - Storoni, Laurent C.

AU - Read, Randy J.

PY - 2007

DA - 2007/07/13 00:00:00

PB - International Union of Crystallography (IUCr)

SP - 658-674

IS - 4

VL - 40

PMID - 19461840

SN - 0021-8898

SN - 1600-5767

ER -

BibTex |

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BibTex Copy

@article{2007_McCoy,

author = {Airlie J. McCoy and Ralf W. Grosse-Kunstleve and Paul D. Adams and Martyn D. Winn and Laurent C. Storoni and Randy J. Read},

title = {Phasercrystallographic software},

journal = {Journal of Applied Crystallography},

year = {2007},

volume = {40},

publisher = {International Union of Crystallography (IUCr)},

month = {jul},

url = {https://doi.org/10.1107%2FS0021889807021206},

number = {4},

pages = {658--674},

doi = {10.1107/S0021889807021206}

}

MLA

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MLA Copy

McCoy, Airlie J., et al. “Phasercrystallographic software.” Journal of Applied Crystallography, vol. 40, no. 4, Jul. 2007, pp. 658-674. https://doi.org/10.1107%2FS0021889807021206.

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Publisher

International Union of Crystallography (IUCr)

Journal

Journal of Applied Crystallography

Quartile SCImago

Quartile WOS

Impact factor

6.1

ISSN

00218898 (Print)
16005767 (Electronic)