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
  • [41] Advances in long-wavelength native phasing at X-ray free-electron lasers
    Nass, Karol
    Cheng, Robert
    Vera, Laura
    Mozzanica, Aldo
    Redford, Sophie
    Ozerov, Dmitry
    Basu, Shibom
    James, Daniel
    Knopp, Gregor
    Cirelli, Claudio
    Martiel, Isabelle
    Casadei, Cecilia
    Weinert, Tobias
    Nogly, Przemyslaw
    Skopintsev, Petr
    Usov, Ivan
    Leonarski, Filip
    Geng, Tian
    Rappas, Mathieu
    Dore, Andrew S.
    Cooke, Robert
    Shirazi, Shahrooz Nasrollahi
    Dworkowski, Florian
    Sharpe, May
    Olieric, Natacha
    Bacellar, Camila
    Bohinc, Rok
    Steinmetz, Michel O.
    Schertler, Gebhard
    Abela, Rafael
    Patthey, Luc
    Schmitt, Bernd
    Hennig, Michael
    Standfuss, Joerg
    Wang, Meitian
    Milne, Christopher J.
    IUCRJ, 2020, 7 : 965 - 975
  • [42] Foreword to the special virtual issue on X-ray free-electron lasers
    Fuoss, Paul H.
    Schlichting, Ilme
    Tschentscher, Thomas
    Yabashi, Makina
    JOURNAL OF SYNCHROTRON RADIATION, 2020, 27 : 576 - 576
  • [44] SwissFEL: The Swiss X-ray Free Electron Laser
    Milne, Christopher J.
    Schietinger, Thomas
    Aiba, Masamitsu
    Alarcon, Arturo
    Alex, Juergen
    Anghel, Alexander
    Arsov, Vladimir
    Beard, Carl
    Beaud, Paul
    Bettoni, Simona
    Bopp, Markus
    Brands, Helge
    Broennimann, Manuel
    Brunnenkant, Ingo
    Calvi, Marco
    Citterio, Alessandro
    Craievich, Paolo
    Csatari Divall, Marta
    Daellenbach, Mark
    D'Amico, Michael
    Dax, Andreas
    Deng, Yunpei
    Dietrich, Alexander
    Dinapoli, Roberto
    Divall, Edwin
    Dordevic, Sladana
    Ebner, Simon
    Erny, Christian
    Fitze, Hansrudolf
    Flechsig, Uwe
    Follath, Rolf
    Frei, Franziska
    Gaertner, Florian
    Ganter, Romain
    Garvey, Terence
    Geng, Zheqiao
    Gorgisyan, Ishkhan
    Gough, Christopher
    Hauff, Andreas
    Hauri, Christoph P.
    Hiller, Nicole
    Humar, Tadej
    Hunziker, Stephan
    Ingold, Gerhard
    Ischebeck, Rasmus
    Janousch, Markus
    Juranic, Pavle
    Jurcevic, Mario
    Kaiser, Maik
    Kalantari, Babak
    APPLIED SCIENCES-BASEL, 2017, 7 (07):
  • [45] Time-resolved protein nanocrystallography using an X-ray free-electron laser
    Aquila, Andrew
    Hunter, Mark S.
    Doak, R. Bruce
    Kirian, Richard A.
    Fromme, Petra
    White, Thomas A.
    Andreasson, Jakob
    Arnlund, David
    Bajt, Sasa
    Barends, Thomas R. M.
    Barthelmess, Miriam
    Bogan, Michael J.
    Bostedt, Christoph
    Bottin, Herve
    Bozek, John D.
    Caleman, Carl
    Coppola, Nicola
    Davidsson, Jan
    DePonte, Daniel P.
    Elser, Veit
    Epp, Sascha W.
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Frank, Matthias
    Fromme, Raimund
    Graafsma, Heinz
    Grotjohann, Ingo
    Gumprecht, Lars
    Hajdu, Janos
    Hampton, Christina Y.
    Hartmann, Andreas
    Hartmann, Robert
    Hauriege, Stefan
    Hauser, Guenter
    Hirsemann, Helmut
    Holl, Peter
    Holton, James M.
    Hoemke, Andre
    Johansson, Linda
    Kimmel, Nils
    Kassemeyer, Stephan
    Krasniqi, Faton
    Kuehnel, Kaiuwe
    Liang, Mengning
    Lomb, Lukas
    Malmerberg, Erik
    Marchesini, Stefano
    Martin, Andrew V.
    Maia, Filipe R. N. C.
    OPTICS EXPRESS, 2012, 20 (03): : 2706 - 2716
  • [46] A revised partiality model and post-refinement algorithm for X-ray free-electron laser data
    Ginn, Helen Mary
    Brewster, Aaron S.
    Hattne, Johan
    Evans, Gwyndaf
    Wagner, Armin
    Grimes, Jonathan M.
    Sauter, Nicholas K.
    Sutton, Geoff
    Stuart, David Ian
    ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2015, 71 : 1400 - 1410
  • [47] Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser
    Wu, Wenting
    Nogly, Przemyslaw
    Rheinberger, Jan
    Kick, Leonhard M.
    Gati, Cornelius
    Nelson, Garrett
    Deupi, Xavier
    Standfuss, Joerg
    Schertler, Gebhard
    Panneels, Valerie
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2015, 71 : 856 - 860
  • [48] Growing Crystals for X-ray Free-Electron Laser Structural Studies of Biomolecules and Their Complexes
    Nanev, Christo N.
    Saridakis, Emmanuel
    Chayen, Naomi E.
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2023, 24 (22)
  • [49] Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses
    Nass, Karol
    Gorel, Alexander
    Abdullah, Malik M.
    Martin, Andrew, V
    Kloos, Marco
    Marinelli, Agostino
    Aquila, Andrew
    Barends, Thomas R. M.
    Decker, Franz-Josef
    Doak, R. Bruce
    Foucar, Lutz
    Hartmann, Elisabeth
    Hilpert, Mario
    Hunter, Mark S.
    Jurek, Zoltan
    Koglin, Jason E.
    Kozlov, Alexander
    Lutman, Alberto A.
    Kovacs, Gabriela Nass
    Roome, Christopher M.
    Shoeman, Robert L.
    Santra, Robin
    Quiney, Harry M.
    Ziaja, Beata
    Boutet, Sebastien
    Schlichting, Ilme
    NATURE COMMUNICATIONS, 2020, 11 (01)
  • [50] Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser
    Nass, Karol
    Bacellar, Camila
    Cirelli, Claudio
    Dworkowski, Florian
    Gevorkov, Yaroslav
    James, Daniel
    Johnson, Philip J. M.
    Kekilli, Demet
    Knopp, Gregor
    Martiel, Isabelle
    Ozerov, Dmitry
    Tolstikova, Alexandra
    Vera, Laura
    Weinert, Tobias
    Yefanov, Oleksandr
    Standfuss, Joerg
    Reiche, Sven
    Milne, Christopher J.
    IUCRJ, 2021, 8 : 905 - 920