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authorThomas White <taw@physics.org>2011-07-28 11:15:45 +0200
committerThomas White <taw@physics.org>2012-02-22 15:27:35 +0100
commite953b109bbe9effa176f70872369f869b6a40699 (patch)
tree776fbb62efc10ae7b2f65f3f5ef047428cb6b90d /README
parent1e84822a59f2c2fffb12ab7614f81dff24df6720 (diff)
Update README
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-rw-r--r--README40
1 files changed, 22 insertions, 18 deletions
diff --git a/README b/README
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@@ -41,12 +41,11 @@ above characteristics. The main programs are:
In addition, there is also:
- - get_hkl, for generating a list of squared structure factors for
- comparison to simulated or experimental data.
+ - get_hkl, for doing various simple operations on reflection lists.
- - powder_plot, for turning an image into a list of reciprocal space
- vector moduli and intensities (i.e. a powder diffraction
- trace).
+ - powder_plot, for turning image or reflection data into a histogram of
+ reciprocal space vector moduli and intensities (i.e. a
+ 1D powder diffraction trace).
- compare_hkl, for working out the differences (e.g. a q-dependent
scaling factor) between two lists of reflections.
@@ -58,7 +57,9 @@ In addition, there is also:
- cubeit, for summing patterns in 3D to inspect the peak profiles.
- - calibrate_detector, which does nothing useful at the moment.
+ - calibrate_detector, for refining detector geometry.
+
+ - partial_sim, for calculating partial reflection intensities.
Included at no extra cost are:
@@ -67,30 +68,32 @@ Included at no extra cost are:
- render_hkl, for turning reflection lists into pretty graphics.
-There is also a big folder of scripts for achieving many related tasks.
+There is also a folder full of scripts for achieving many related tasks.
-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). There is a script for turning a plain text reflection list into an
-MTZ file for later import into CCP4.
+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.
-For documentation on the individual programs and topics, see the files inside
-the "doc" directory.
+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:
+system. In short, it's the usual:
$ ./configure
$ make
$ make check
$ sudo make install
-You might want to substitute something based on one of the following for the
-first step:
+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
@@ -142,8 +145,9 @@ 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, the Capitalisation
-Monster will hunt you down and eat you.
+"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