From 3761e1f1e07b14c3d2b105ceccb231e053d025ad Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 5 Mar 2021 11:10:02 +0100 Subject: Switch to markdown for README --- README | 208 ----------------------------------------------------------------- 1 file changed, 208 deletions(-) delete mode 100644 README (limited to 'README') diff --git a/README b/README deleted file mode 100644 index d74ea8c6..00000000 --- a/README +++ /dev/null @@ -1,208 +0,0 @@ -CrystFEL - Data processing for serial crystallography ------------------------------------------------------ - -Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY, - a research centre of the Helmholtz Association. - -Authors: - Thomas White - Richard Kirian - Kenneth Beyerlein - Andrew Aquila - Andrew Martin - Lorenzo Galli - Chun Hong Yoon - Kenneth Beyerlein - Karol Nass - Nadia Zatsepin - Anton Barty - Cornelius Gati - Fedor Chervinskii - Alexandra Tolstikova - Wolfgang Brehm - Valerio Mariani - Parker de Waal - Takanori Nakane - Keitaro Yamashita - Mamoru Suzuki - Thomas Grant - Steve Aplin - Oleksandr Yefanov - Helen Ginn - Nicolas Riebesel - Yaroslav Gevorkov - Omri Mor - --------------------------------------------------------------------------------- - -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 -version. - -CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY -WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A -PARTICULAR PURPOSE. See the GNU General Public License for more details. - -You should have received a copy of the GNU General Public License along with -CrystFEL. If not, see . - --------------------------------------------------------------------------------- - -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. Some of the particular -characteristics of such data which call for a specialised software suite are: - -- 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. - -- The crystal orientations in each pattern are random and uncorrelated, meaning - that: - -- Merging into lower symmetry point groups may require the resolution of - indexing ambiguities. - - -CrystFEL includes programs for simulating and processing patterns subject to the -above characteristics. The main data processing pipeline is defined by four -programs: - - - indexamajig, for bulk indexing and integration of diffraction patterns - - - process_hkl, for quickly merging per-pattern lists of intensities into - a single reflection list - - - partialator, for merging patterns more accurately (and much more - slowly) using scaling, partiality modelling and - post refinement - - - ambigator, for resolving indexing ambiguities - -There are two tools for calculating figures of merit for reflection data: - - - compare_hkl, for figures of merit that involve comparing two sets of - data, like CC* and R_split - - - check_hkl, for figures of merit based on only one set of data, like - completeness, redundancy and twinning tests - -Three tools are provided for visualising data: - - - cell_explorer, for examining distributions of lattice parameters - - - hdfsee, an image viewer - - - render_hkl, for turning reflection lists into pretty graphics - -CrystFEL can also simulate data, e.g. for methods development: - - - pattern_sim, which performs a Fourier image calculation - - - partial_sim, which calculates reflection intensities based on a - partiality calculation and optionally plots the peaks - in an image - -There are also five utility programs: - - - get_hkl, for doing various simple operations on reflection lists such - as expanding by symmetry or adding noise - - - cell_tool, for doing operations on unit cells such as applying - transformations or looking for indexing ambiguities - - - geoptimiser, for refining detector geometry. - - - list_events, for creating event lists from multi-event files. - - - make_pixelmap, for creating HDF5 pixel map files for other programs - like Cheetah and OnDA - - - whirligig, for finding multiple shots from single crystals. - - -There is also a folder full of scripts for achieving many related tasks, such as -file format conversion. - -Standard "man" pages are provided for documentation, or you can invoke any -program with the argument "--help" to get a summary of options. There are some -example geometry and beam description files in doc/examples, and API -documentation created using Doxygen. - - -Installation ------------- - -The terse installation instructions below should be enough if you're experienced -with installing software from source. More detailed installation information is -available on the website: -https://www.desy.de/~twhite/crystfel/install.html - -Mandatory dependencies: - - CMake 3.12 or later - - HDF5 1.8.0 or later (1.10.0 or later preferred) - - GNU Scientific Library (GSL) - - Bison 2.6 or later - - Flex - - Zlib (1.2.3.5 or later preferred) - -"Optional" dependencies: - - GTK2 or later (GTK3 preferred) - - Cairo - - Pango - - gdk-pixbuf - - NCurses - - libPNG - - libTIFF - - FFTW3 - - XGandalf (https://stash.desy.de/users/gevorkov/repos/xgandalf) - -"Optional" run-time dependencies: - - Mosflm (https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/) - - DirAx (http://www.crystal.chem.uu.nl/distr/dirax/) - - XDS (http://xds.mpimf-heidelberg.mpg.de/) - -Note that "optional" means that you *can* install CrystFEL without them, however -your installation will lack important components such as the visualisation -tools and certain indexing algorithms. - -For processing electron diffraction or wide-bandwidth X-ray data, you should -also install PinkIndexer from: -https://stash.desy.de/users/gevorkov/repos/pinkindexer - -Installation follows the normal CMake procedure: - -$ mkdir build -$ cd build -$ cmake .. -$ make -$ sudo make install - -If external libraries have been installed in non-standard locations, you can set -the path like this, for example for Xgandalf: - cmake -DXGANDALF_INCLUDES=/path/to/xgandalf/include \ - -DXGANDALF_LIBRARIES=/path/to/xgandalf/lib/libxgandalf.so - -The path to HDF5 can be set similarly: - cmake -DHDF5_ROOT=/path/to/hdf5 (... /include, /lib etc) - -To install CrystFEL in a custom location, use: - cmake -DCMAKE_INSTALL_PREFIX=/path/for/crystfel/installation - - -Funding acknowledgements ------------------------- - -Development of CrystFEL is primarily funded by the Helmholtz Association. - -Partial funding for CrystFEL has previously been provided by: - -- "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