From c770af15a304fd88efdfe82250e43a28b0353e77 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Tue, 22 Jun 2010 19:04:01 +0200 Subject: Update README --- README | 63 +++++++++++++++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 55 insertions(+), 8 deletions(-) diff --git a/README b/README index 2b178e52..86b5ce10 100644 --- a/README +++ b/README @@ -5,7 +5,7 @@ Thomas White , 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 +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 @@ -16,20 +16,19 @@ characteristics of such data which call for a specialised software suite are - Many patterns (>10,000) are required - high throughput is needed. - -The main programs are: +CrystFEL includes programs for simulating and processing patterns subject to the +above characteristics. The main programs are: - pattern_sim, for simulating patterns. - - indexamajig, for finding hits, locating peaks, indexing patterns - and constructing lists of h,k,l,I,sigma(I) for each - pattern. + - 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. - - hdfsee, a simple HDF5 image viewer. - In addition, there is also: - get_hkl, for generating a list of squared structure factors for @@ -41,3 +40,51 @@ In addition, there is also: - 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. -- cgit v1.2.3