Development of “Parameter space screening”-based single-wavelength anomalous diffraction phasing and structure determination pipeline

doi:10.1088/1674-1056/ab43bd

中国物理B ›› 2019, Vol. 28 ›› Issue (11): 116101-116101.doi: 10.1088/1674-1056/ab43bd

• CONDENSED MATTER: STRUCTURAL, MECHANICAL, AND THERMAL PROPERTIES • 上一篇下一篇

Development of “Parameter space screening”-based single-wavelength anomalous diffraction phasing and structure determination pipeline

Wei Ding(丁玮), Xiao-Ting Wang(王小婷), Yang-Yang Yi(易阳旸)

1 Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China;
2 School of Environment, Tsinghua University, Beijing 100084, China;
3 School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, China

收稿日期:2019-08-12 修回日期:2019-09-03 出版日期:2019-11-05 发布日期:2019-11-05
通讯作者: Wei Ding E-mail:dingwei@iphy.ac.cn

Development of “Parameter space screening”-based single-wavelength anomalous diffraction phasing and structure determination pipeline

Wei Ding(丁玮)^1,2, Xiao-Ting Wang(王小婷)², Yang-Yang Yi(易阳旸)³

1 Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China;
2 School of Environment, Tsinghua University, Beijing 100084, China;
3 School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, China

Received:2019-08-12 Revised:2019-09-03 Online:2019-11-05 Published:2019-11-05
Contact: Wei Ding E-mail:dingwei@iphy.ac.cn

摘要/Abstract

摘要： In this paper, we present a highly efficient structure determination pipeline software suite (X²DF) that is based on the “Parameter space screening” method, by combining the popular crystallographic structure determination programs and high-performance parallel computing. The phasing method employed in X²DF is based on the single-wavelength anomalous diffraction (SAD) theory. In the X²DF, the choice of crystallographic software, the input parameters to this software and the results display layout, are all parameters which users can select and screen automatically. Users may submit multiple structure determination jobs each time, and each job uses a slightly different set of input parameters or programs. Upon completion, the results of the calculation performed can be displayed, harvested, and analyzed by using the graphical user interface (GUI) of the system. We have applied the X²DF successfully to many cases including the cases that the structure solutions fail to be yielded by using manual approaches.

关键词: single-wavelength anomalous diffraction, parameter space screening method, structure determination pipeline

Abstract: In this paper, we present a highly efficient structure determination pipeline software suite (X²DF) that is based on the “Parameter space screening” method, by combining the popular crystallographic structure determination programs and high-performance parallel computing. The phasing method employed in X²DF is based on the single-wavelength anomalous diffraction (SAD) theory. In the X²DF, the choice of crystallographic software, the input parameters to this software and the results display layout, are all parameters which users can select and screen automatically. Users may submit multiple structure determination jobs each time, and each job uses a slightly different set of input parameters or programs. Upon completion, the results of the calculation performed can be displayed, harvested, and analyzed by using the graphical user interface (GUI) of the system. We have applied the X²DF successfully to many cases including the cases that the structure solutions fail to be yielded by using manual approaches.

Key words: single-wavelength anomalous diffraction, parameter space screening method, structure determination pipeline

中图分类号: (Techniques for structure determination)

61.05.-a

丁玮, 王小婷, 易阳旸. Development of “Parameter space screening”-based single-wavelength anomalous diffraction phasing and structure determination pipeline[J]. 中国物理B, 2019, 28(11): 116101-116101.

Wei Ding(丁玮), Xiao-Ting Wang(王小婷), Yang-Yang Yi(易阳旸). Development of “Parameter space screening”-based single-wavelength anomalous diffraction phasing and structure determination pipeline[J]. Chin. Phys. B, 2019, 28(11): 116101-116101.

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Development of “Parameter space screening”-based single-wavelength anomalous diffraction phasing and structure determination pipeline

Development of “Parameter space screening”-based single-wavelength anomalous diffraction phasing and structure determination pipeline

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