On the release of cppxfel for processing X-ray free-electron laser images

被引:25
|
作者
Ginn, Helen Mary [1 ]
Evans, Gwyndaf [2 ]
Sauter, Nicholas K. [3 ]
Stuart, David Ian [1 ,2 ]
机构
[1] Wellcome Trust Ctr Human Genet, Div Struct Biol, Roosevelt Dr, Oxford OX3 7BN, Oxon, England
[2] Diamond House,Harwell Sci & Innovat Campus, Didcot OX11 QX, Oxon, England
[3] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, 1 Cyclotron Rd, Berkeley, CA 94720 USA
基金
英国医学研究理事会; 英国惠康基金;
关键词
X-ray free-electron lasers; XFELS; serial femtosecond crystallography; data analysis; computer programs; CRYSTALLOGRAPHIC DATA; POST-REFINEMENT; PHOTOSYSTEM-II; FEMTOSECOND; DIFFRACTION; MODEL;
D O I
10.1107/S1600576716006981
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.
引用
收藏
页码:1065 / 1072
页数:8
相关论文
共 50 条
  • [21] TEACHING THE PRINCIPLES AND APPLICATIONS OF X-RAY FREE-ELECTRON LASER RADIATION
    Tschentscher, Th.
    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2002, 58 : C199 - C199
  • [22] Focus characterization of an X-ray free-electron laser by intensity correlation measurement of X-ray fluorescence
    Nakamura, Nami
    Matsuyama, Satoshi
    Inoue, Takato
    Inoue, Ichiro
    Yamada, Jumpei
    Osaka, Taito
    Yabashi, Makina
    Ishikawa, Tetsuya
    Yamauchi, Kazuto
    JOURNAL OF SYNCHROTRON RADIATION, 2020, 27 : 1366 - 1371
  • [23] RADDOSE-XFEL: femtosecond time-resolved dose estimates for macromolecular X-ray free-electron laser experiments
    Dickerson, Joshua L.
    McCubbin, Patrick T. N.
    Garman, Elspeth F.
    JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2020, 53 : 549 - 560
  • [24] X-ray diffraction from strongly bent crystals and spectroscopy of X-ray free-electron laser pulses
    Kaganer, Vladimir M.
    Petrov, Ilia
    Samoylova, Liubov
    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2020, 76 : 55 - 69
  • [25] Data acquisition system for X-ray free-electron laser experiments at SACLA
    Joti, Yasumasa
    Kameshima, Takashi
    Yamaga, Mitsuhiro
    Sugimoto, Takashi
    Okada, Kensuke
    Abe, Toshinori
    Furukawa, Yukito
    Ohata, Toru
    Tanaka, Ryotaro
    Hatsui, Takaki
    Yabashi, Makina
    JOURNAL OF SYNCHROTRON RADIATION, 2015, 22 : 571 - 576
  • [26] Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser
    Beyerlein, Kenneth R.
    Jonsson, H. Olof
    Alonso-Mori, Roberto
    Aquila, Andrew
    Barty, Sasa
    Barty, Anton
    Bean, Richard
    Koglin, Jason E.
    Messerschmidt, Marc
    Ragazzon, Davide
    Sokaras, Dimosthenis
    Williams, Garth J.
    Hau-Riege, Stefan
    Boutet, Sebastien
    Chapman, Henry N.
    Imneanu, Nicusor T.
    Caleman, Carl
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2018, 115 (22) : 5652 - 5657
  • [27] Technology of precise irradiation timing for X-ray free-electron laser (XFEL)
    Otake, Yuji
    Seimitsu Kogaku Kaishi/Journal of the Japan Society for Precision Engineering, 2009, 75 (12): : 1391 - 1395
  • [28] Focusing femtosecond X-ray free-electron laser pulses by refractive lenses
    Kohn, V. G.
    JOURNAL OF SYNCHROTRON RADIATION, 2012, 19 : 84 - 92
  • [29] Mirror Vibration Tolerance Studies in X-ray Free-Electron Laser Oscillator
    Li, Shaohua
    Huang, Nanshun
    Zhou, Jianyang
    Deng, Haixiao
    PHOTONICS, 2023, 10 (09)
  • [30] Polarization control of an X-ray free-electron laser with a diamond phase retarder
    Suzuki, Motohiro
    Inubushi, Yuichi
    Yabashi, Makina
    Ishikawa, Tetsuya
    JOURNAL OF SYNCHROTRON RADIATION, 2014, 21 : 466 - 472