CrystFEL - Crystallography with a FEL ------------------------------------- Copyright © 2012-2013 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 Please read the AUTHORS file for a full list of contributions and contributors. See the COPYING file for licence conditions. Summary: GPLv3+. Thank you for reading the documentation. :-) CrystFEL is a suite of programs for processing (and simulating) Bragg diffraction data acquired with a 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. Unique correction factors are needed. - The crystals are small, leading to significant Fourier truncation effects on the detector. - Many patterns (>10,000) 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 programs are: - pattern_sim, for simulating patterns. - indexamajig, a "batch indexer" and data reduction program. It is used for finding hits, locating peaks, indexing patterns and constructing lists of h,k,l,I,sigma(I) (or similar) for each pattern. - process_hkl, for merging per-pattern lists of intensities into a single reflection list. - partialator, for merging patterns more accurately (and much more slowly) using post refinement. In addition, there is also: - get_hkl, for doing various simple operations on reflection lists. - compare_hkl, for working out the differences (e.g. a q-dependent scaling factor) between two lists of reflections. - check_hkl, for determining things like completeness. - partial_sim, for calculating partial reflection intensities. Included at no extra cost are: - hdfsee, a simple viewer for images stored in HDF5 format. - render_hkl, for turning reflection lists into pretty graphics. There is also a folder full of scripts for achieving many related tasks. CrystFEL mostly works with images stored in HDF5 format, unit cell data in PDB format, and reflection lists in plain text format (i.e. not MTZ). There are scripts for converting both ways between plain text reflection lists and MTZ files. 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 development documentation created using GTK-Doc. Installation ------------ See the "INSTALL" file for the generic instructions on how to use the build system. In short, it's the usual: $ ./configure $ make $ make check $ sudo make install If you have libraries installed in strange places, you might want to do something similar to one of these instead of the first step: $ ./configure --with-opencl $ ./configure --with-hdf5=/some/strange/location $ ./configure --with-libtiff=/some/strange/location $ ./configure --with-gsl=/some/strange/location $ ./configure --disable-gtk At a minimum, you will need the HDF5 library (version 1.8.0 or later) and the GNU Scientific Library (GSL). For a full installation, you will also need libTIFF, libPNG, Cairo and GTK. You must use an installation of the HDF5 library which is thread safe. That means it must have been configured with the "--enable-threadsafe" option. Most binary distributions appear NOT to be like this. If you don't have a thread safe HDF5 library, just be sure not to use the "-j" option for any of the CrystFEL programs. If you're compiling on Mac OS X, where GTK, libPNG and libTIFF seem to be much harder to come by, disable lots of things: $ ./configure --disable-gtk --disable-png --disable-libtiff If you get an error mentioning fftw3 and telling you to recompile with -fPIC, then your version of FFTW3 is not compiled in a suitable way. You'll need to install it again (from source) adding "--enable-shared" to its ./configure command line. If you get an error about "cairo_surface_show_page" in src/scaling-report.c, simply edit the file and comment that line out. Partialator will then not be able to produce a useful scaling report, but the rest of CrystFEL will work properly. If you are installing from Git, the following extra things apply: - You must run "./autogen.sh" to generate "configure" and other files before proceeding as detailed above. - If you have an old version of Automake (less than 1.10), or an old version of Autoconf (less than 2.60), you'll need to add the following line near the top of Makefile.am: docdir = ${datadir}/doc/${PACKAGE} - If your Automake version is less than 1.11, you'll need to comment out the reference to AM_SILENT_RULES in configure.ac, like this: dnl AM_SILENT_RULES([yes]) - You will not be able to use the "--enable-gtk-doc" option to configure unless you have at least version 1.9 of gtk-doc installed. Program name ------------ There seems to be a tendency to capitalise all the letters in the names of programs in scientific publications. Sometimes the authors do this, other times the journal capitalises them at the proof stage. It's as if they think it somehow makes the name look more "computery", or perhaps "trademark-y". Well, it's not 1970 any more, and programs are no longer input on punched cards. That means we can have capitalisation any way we choose. The name for the overall software suite is "CrystFEL", with this being the only acceptable capitalisation. The individual programs should always be referred to with all letters in lower case, exactly the same as the names of the binaries. Put the names in quotes or italics if this sounds strange to you. The only exception is if the name of the program comes at the start of a sentence, or in a title, or similar position where a word would normally be capitalised. In most cases, it will be more appropriate to refer to the overall suite than to one of its constituent programs. The following are NOT acceptable forms: "CRYSTFEL", "crystFEL", "Crystfel", "INDEXAMAJIG" and "PATTERN_SIM". If you use any of these (particularly the first one and the last two), the Capitalisation Monster will hunt you down and eat you. In addition, CrystFEL is made up of "programs", not "routines" nor "procedures". (The "programs" in turn are made up from "routines" and "procedures", but unless you are exploring the source code, there's no need for you to know about that). I hope you can forgive the fussiness.