From 7607fcb686300e0e8b89ed92a38ad8cb94b0be34 Mon Sep 17 00:00:00 2001 From: Takanori Nakane Date: Fri, 3 Jul 2020 14:18:30 +0100 Subject: [PATCH] GUI: Update citations --- src/gui_mainwindow.cpp | 103 ++++++++++++++++++++++------------------- 1 file changed, 56 insertions(+), 47 deletions(-) diff --git a/src/gui_mainwindow.cpp b/src/gui_mainwindow.cpp index 7dec53049..e202ad172 100644 --- a/src/gui_mainwindow.cpp +++ b/src/gui_mainwindow.cpp @@ -3446,63 +3446,72 @@ void GuiMainWindow::cb_about(Fl_Widget* o, void* v) void GuiMainWindow::cb_about_i() { -#define HELPTEXT ("RELION " RELION_SHORT_VERSION "\n \n \ -RELION is is developed in the groups of\n\n \ -Sjors H.W. Scheres at the MRC Laboratory of Molecular Biology\n \n \ -- Sjors H.W. Scheres\n \ -- Shaoda He\n \ -- Takanori Nakane\n \ -- Jasenko Zivanov\n \ -- Liyi Dong\n \ -\n \n \ -and Erik Lindahl at Stockholm University\n \n \ -- Erik Lindahl\n \ -- Björn O. Forsberg\n \ -- Dari Kimanius\n \ +#define HELPTEXT ("RELION " RELION_SHORT_VERSION " \n\n\ +RELION is developed in the groups of:\n\n\ +Sjors H.W. Scheres at the MRC Laboratory of Molecular Biology\n\ + - Sjors H.W. Scheres\n\ + - Shaoda He\n\ + - Takanori Nakane\n\ + - Jasenko Zivanov\n\ + - Liyi Dong\n\ + - Dari Kimanius\n\ +\n\ +and Erik Lindahl at Stockholm University\n\ + - Erik Lindahl\n\ + - Björn O. Forsber\n\ \n\ Note that RELION is completely free, open-source software. You can redistribute it and/or modify it for your own purposes, but please do make sure \ the contribution of the developers are acknowledged appropriately. In order to maintain an overview of existing versions, a notification regarding \ -any redistribution of (modified versions of) the code is appreciated (contact Sjors directly). \n \n \n \ +any redistribution of (modified versions of) the code is appreciated (contact Sjors directly).\n\n\ If RELION is useful in your work, please cite us. Relevant papers are:\n \n \ - * General Bayesian approach (and first mention of RELION): \n \ - Scheres (2012) J. Mol. Biol. (PMID: 22100448) \n \n\ - * RELION implementation details and the 3D auto-refine procedure: \n \ - Scheres (2012) J. Struct. Biol. (PMID: 23000701) \n \n\ - * Gold-standard FSC and the relevance of the 0.143 criterion: \n \ - Scheres & Chen (2012) Nat. Meth. (PMID: 22842542) \n \n\ - * Movie-processing procedure: \n \ - Bai et al. (2013) eLife (PMID: 23427024 ) \n \n\ - * Correction of mask effects on the FSC curve by randomised phases: \n \ - Chen et al. (2013) Ultramicroscopy (PMID: 23872039) \n \n\ - * Auto-picking : \n \ - Scheres (2014) J. Struct. Biol. (PMID: 25486611) \n \n \ - * Sub-tomogram averaging : \n \ - Bharat et al. (2015) Structure (PMID: 26256537) \n \n \ - * v.2.0 GPU capability and autopicking acceleration : \n \ - Kimanius et al. (2016) eLife (PMID: 27845625) \n \n \ - * Helical reconstruction : \n \ - He & Scheres (2017) J, Struct. Biol. (PMID: 28193500) \n \n \ -Please also cite the following EXTERNAL programs: \n \n \ -* MOTIONCOR2 for beam-induced motion correction: \n \ - Zheng et al (2017) Nat. Meth. (PMID: 28250466) \n \n\ -* UNBLUR for beam-induced motion correction: \n \ - Grabnt & Grigorieff eLife (PMID: 26023829) \n \n\ -* CTFFIND4 for CTF-estimation: \n \ - Rohou & Grigorieff (2015) J. Struct. Biol. (PMID: 26278980) \n \n\ -* Gctf for CTF-estimation: \n \ - Zhang (2016) J. Struct. Biol. (PMID: 26592709) \n \n\ -* Stochastic Gradient Descent initial model generation: \n\ - Punjani et al. (2017) Nat. Meth. (PMID: 28165473) \n \n\ -* ResMap for local-resolution estimation: \n\ - Kucukelbir et al. (2014) Nat. Meth. (PMID: 24213166) \n \n\ -* Postscript plots are made using CPlot2D from www.amzsaki.com\n\n\ + * General Bayesian approach (and first mention of RELION):\n\ + Scheres (2012) J. Mol. Biol. (PMID: 22100448)\n\n\ + * RELION implementation details and the 3D auto-refine procedure:\n\ + Scheres (2012) J. Struct. Biol. (PMID: 23000701)\n\n\ + * Gold-standard FSC and the relevance of the 0.143 criterion:\n\ + Scheres & Chen (2012) Nat. Meth. (PMID: 22842542)\n\n\ + * Correction of mask effects on the FSC curve by randomised phases:\n\ + Chen et al. (2013) Ultramicroscopy (PMID: 23872039)\n\n\ + * Auto-picking :\n\ + Scheres (2014) J. Struct. Biol. (PMID: 25486611)\n\n\ + * Sub-tomogram averaging :\n\ + Bharat et al. (2015) Structure (PMID: 26256537)\n\n\ + * RELION 2.0 GPU capability and autopicking acceleration:\n\ + Kimanius et al. (2016) eLife (PMID: 27845625)\n\n\ + * Helical reconstruction:\n\ + He & Scheres (2017) J, Struct. Biol. (PMID: 28193500)\n\n\ + * RELION 3.0 CTFRefine, RelionIt, CPU acceleration, Ewald sphere correction:\n\ + Zivanov et al. (2018) eLife (PMID: 30412051)\n\n\ + * Multibody refinement:\n\ + Nakane et al. (2018) eLife (PMID: 29856314)\n\n\ + * Bayesian Polishing:\n\ + Zivanov et al. (2019) IUCrJ (PMID: 30713699)\n\n\ + * Higher-order aberration correction, magnification anisotropy correction\n\ + Zivanov et al. (2020) IUCrJ (PMID: 32148853)\n\n\ + * Amyloid structure determination:\n\ + Scheres (2020) Acta Crystallor. D (PMID: 32038040)\n\n\ +\ +Please also cite relevant papers when you used external programs or their algorithms re-implemented in RELION: \n \n \ +* MOTIONCOR2 algorithm for beam-induced motion correction:\n\ + Zheng et al (2017) Nat. Meth. (PMID: 28250466)\n\n\ +* CTFFIND4 for CTF-estimation:\n\ + Rohou & Grigorieff (2015) J. Struct. Biol. (PMID: 26278980)\n\n\ +* GCTF for CTF-estimation:\n\ + Zhang (2016) J. Struct. Biol. (PMID: 26592709)\n\n\ +* Stochastic Gradient Descent for initial model generation:\n\ + Punjani et al. (2017) Nat. Meth. (PMID: 28165473)\n\n\ +* ResMap for local-resolution estimation:\n\ + Kucukelbir et al. (2014) Nat. Meth. (PMID: 24213166)\n\n\ +* Symmetry relaxation:\n\ + Abrishami et al. (2020) Prog. Biophys. Mol. Biol. (PMID: 32470354) \n\n\ +* Postscript plots are made using CPlot2D from http://www.amzsaki.com\n\n\ \ About the start up screen:\n\n\ The map shown is the cryo-EM map of mouse heavy-chain apoferritin\n\ at 1.54 A (EMDB-9865). This is the highest resolution single particle\n\ reconstruction map deposited to EMDB as of August 2019. The raw dataset\n\ is also available at EMPIAR-10248.\ - ") +") ShowHelpText *help = new ShowHelpText(HELPTEXT); }