From 9604bffbb66b3d920ea677701e54ef032a36e572 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 3 Mar 2023 11:23:59 +0100 Subject: Update README.md --- README.md | 136 ++++++++++++++++++++++++++++++++++++++++++++------------------ 1 file changed, 97 insertions(+), 39 deletions(-) diff --git a/README.md b/README.md index f3636672..9a4760e8 100644 --- a/README.md +++ b/README.md @@ -1,43 +1,119 @@ CrystFEL - Data processing for serial crystallography ===================================================== -Copyright © 2012-2023 Deutsches Elektronen-Synchrotron DESY, - a research centre of the Helmholtz Association. +Overview +-------- -See AUTHORS as well as individual source code files for full details of contributors. +CrystFEL is a suite of programs for processing data from [serial +crystallography experiments](https://en.wikipedia.org/wiki/Serial_Femtosecond_Crystallography), +performed at synchrotron and X-ray free-electron laser facilities, as well as +in your home lab using an electron microscope. -Introduction ------------- -CrystFEL is a suite of programs for processing (and simulating) Bragg -diffraction data from "serial crystallography" experiments, often (but not -always) performed using an X-ray Free-Electron Laser. Compared to rotation data, -some of the particular characteristics of such data which call for a -specialised software suite are: +Getting started +--------------- + +See [INSTALL.md](INSTALL.md) for installation instructions, including +installation via package manager and details of pre-existing installations at +X-ray facilities around the world. + +CrystFEL can be used from the command line or via a graphical user interface. +To start the graphical user interface, run ```crystfel```. + +There is a [video tutorial](https://vimeo.com/585412404), as well as a [text +tutorial](doc/articles/tutorial.rst) to get you started with processing via the +GUI. + +For command-line use, standard ```man``` pages are available. Start with +```man crystfel```. The manual pages are also +[available on the web](https://www.desy.de/~twhite/crystfel/manual.html). + + +Documentation +------------- + +* [Basic Tutorial](doc/articles/tutorial.rst) +* [How to choose the right point group for merging](doc/articles/pointgroup.rst) +* [How to increase data processing speed](doc/articles/speed.rst) +* [Real-time data processing](doc/articles/online.rst) +* [Processing electron diffraction data](doc/articles/electrons.rst) +* [Symmetry classification for serial crystallography](doc/twin-calculator.pdf) +* [Matrix conventions used in CrystFEL code](doc/matrix-notation.pdf) - for + developers, written mostly for my own benefit. +* [Hit rate graph](doc/hitrate.png) +* [Examples folder](doc/examples) - contains some template input files. +* [Contributing to CrystFEL](CONTRIBUTING.md) - including how to cite CrystFEL + and how to find good first issues to work on. +* [Citation list](https://www.desy.de/~twhite/crystfel/citations.html) - please + send us details of your paper, if it's missing! +* [Scripts folder](scripts) - a miscellany of smaller programs to help at + various stages of data processing. + + +Journal articles and book chapters +---------------------------------- + +* [Processing serial crystallography data with CrystFEL: a step-by-step + guide](https://doi.org/10.1107/S205979831801238X) - covers command-line + processing only (pre-dates the GUI). +* [Recent developments in CrystFEL](http://dx.doi.org/10.1107/S1600576716004751) - + now somewhat out of date, but contains some useful information about the + algorithms used. +* [Crystallography and Molecular Imaging using X-ray + Lasers](https://doi.org/10.23730/CYRSP-2018-001.605) - an introduction to the + biological aspects and possibilities, written for physicists (in contrast to + most other articles, which introduce the physical aspects for biologists!). +* [Original paper about CrystFEL](http://dx.doi.org/10.1107/S0021889812002312) + from 2012. Not open access, but a "reprint" is available + [here](https://www.desy.de/~twhite/crystfel/db5097-reprint.pdf). +* [Climbing the Data Mountain: Processing of SFX + Data](https://link.springer.com/chapter/10.1007/978-3-030-00551-1_7) - + emphasizes data volume issues for XFELs. Unfortunately not open access. +* [Processing of XFEL + Data](https://link.springer.com/protocol/10.1007/978-1-4939-7000-1_13) - + describes the entire processing pipeline. Unfortunately not open access. + + +Awards +------ + +In 2017, the development of CrystFEL was recognised with the [Max von Laue +Prize](https://www.desy.de/news/news_search/index_eng.html?openDirectAnchor=1202) +from the [German Society for Crystallography (DGK)](https://dgk-home.de/en/). -* The sliced, rather than integrated, measurement of intensity data. Many, if - not all reflections are partially integrated. -* Many patterns (thousands) are required - high throughput is needed. +Funding acknowledgements +------------------------ -* The crystal orientations in each pattern are random and uncorrelated. +Development of CrystFEL is primarily funded by the +[Helmholtz Association](https://www.helmholtz.de/) via +[DESY](https://www.desy.de/). -* Merging into lower symmetry point groups may require the resolution of - indexing ambiguities. +Partial funding for CrystFEL has previously been provided by: +* European Union’s Horizon 2020 research and innovation programme under grant + agreement No 857641 ([ExPaNDS](https://expands.eu/)) (2019-2023). -Getting started ---------------- +* [X-Probe](http://x-probe.org/), a project of the European Union's 2020 + Research and Innovation Program Under the Marie Skłodowska-Curie grant + agreement 637295 (2015-2018). -See INSTALL.md for installation instructions. +* The [BMBF](https://www.bmbf.de/) German-Russian Cooperation + [SyncFELMed](http://www.syncfelmed.org/), grant 05K14CHA (2014-2017). -The best way to get started, after installation, is to run command ```crystfel``` -to start the graphical user interface. +* [BioStruct-X](https://www.biostruct-x.eu/), a project funded by the Seventh + Framework Programme (FP7) of the European Commission (2011-2016). Licence ------- +Copyright © 2012-2023 Deutsches Elektronen-Synchrotron DESY, a research centre +of the Helmholtz Association. + +See [AUTHORS](AUTHORS) as well as individual source code files for full details +of contributors. + CrystFEL is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later @@ -51,21 +127,3 @@ You should have received a copy of the GNU General Public License along with CrystFEL. If not, see . -Funding acknowledgements ------------------------- - -Development of CrystFEL is primarily funded by the Helmholtz Association. - -Partial funding for CrystFEL has previously been provided by: - -- European Union’s Horizon 2020 research and innovation programme under grant - agreement No 857641 (ExPaNDS) (2019-2023). - -- "X-Probe", a project of the European Union's 2020 Research and Innovation - Program Under the Marie Skłodowska-Curie grant agreement 637295 (2015-2018). - -- The BMBF German-Russian Cooperation "SyncFELMed", grant 05K14CHA (2014-2017). - -- BioStruct-X, a project funded by the Seventh Framework Programme (FP7) of the - European Commission (2011-2016). - -- cgit v1.2.3