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CrystFEL - Crystallography with a FEL
-------------------------------------
Thomas White <taw@physics.org>, CFEL, DESY
CrystFEL is a suite of programs for simulating and processing crystallographic
(Bragg diffraction) data acquired with a free electron laser. 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.
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.
In addition, there is also:
- get_hkl, for generating a list of squared structure factors for
comparison to simulated or experimental data.
- powder_plot, for turning an image into a list of reciprocal space
vector moduli and intensities (i.e. a powder diffraction
trace).
- compare_hkl, for working out the differences (e.g. a q-dependent
scaling factor) between two lists of reflections.
And, because I'm so nice, included at no extra cost is:
- hdfsee, a simple viewer for images stored in HDF5 format.
CrystFEL mostly works with images stored in HDF5 format, unit cell and atomic
coordinate data in PDB format, and reflection lists in plain text format (i.e.
not MTZ).
For documentation on the individual programs, see the files inside the "doc"
directory.
Installation
------------
See the "INSTALL" file for the generic instructions on how to use the build
system. In short, it's
$ ./configure
$ make
$ sudo make install
You might want to substitute something based on one of the following for the
first step:
$ ./configure --enable-opencl
$ ./configure --with-hdf5=/some/strange/location
$ ./configure --with-libtiff=/some/strange/location
$ ./configure --with-gsl=/some/strange/location
$ ./configure --disable-gtk
A note on data orientation
--------------------------
CrystFEL defines "x" as the most quickly varying coordinate in the data, and "y"
as the second most quickly varying coordinate in the data. It doesn't know what
to do with any extra dimensions beyond the second.
The origin, which is considered the lower left corner of the image, is defined
by CrystFEL as the first element in the image data. Positive x points in a
direction to the right, and positive y points upwards. When a right-handed
coordinate system is formed using these definitions, CrystFEL will consider the
positive z direction to point towards the source of the incident beam.
The detector surface is assumed to be perpendicular to the incident beam.
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