Add to the documentation

1 files changed, 10 insertions, 11 deletions

diff --git a/doc/man/pattern_sim.1 b/doc/man/pattern_sim.1
index d53aeae5..b9c8fa33 100644
--- a/doc/man/pattern_sim.1
+++ b/doc/man/pattern_sim.1
@@ -16,21 +16,20 @@ pattern\_sim \- Simulation of nanocrystallographic diffraction patterns
 
 .SH DESCRIPTION
 
-pattern_sim does not know about symmetry, so your input reflection list
-(give with "-i") must be expanded.  You can do this with:
+Pattern_sim simulaties diffraction patterns from small crystals probed with femtosecond pulses of X-rays from a free electron laser.  Typical use might be of the form:
 
-$ get_hkl -i myfile.hkl -o output.hkl -y mypointgroup -e 1
+pattern_sim -g mydetector.geom -b my.beam -p my.pdb -r -i myintensities.hkl
+
+The unit cell geometry will be taken from the CRYST1 line in the PDB file you provide, and the intensities of the reflections will be interpolated from the reflection list file you provide.  The reflection list format is the same as that output by process_hkl and handled by get_hkl.  You also need beam and geometry description files (-b and -g respectively).  See `man crystfel_geometry' for details of how to create a geometry file.  Examples of both files can be found in the installation directory, which is normally /usr/local/share/doc/crystfel.
 
-get_hkl does not currently understand symmetry, which means you'll have to
-expand any molecular model (the PDB) out to P1 to get the correct results.  You
-can achieve that, for example, by loading it into Mercury, turning on "Packing"
-and re-saving.  Alternatively, you can do this using CCP4 with a command like:
+The result will be written to an HDF5 file in the current directory with the name `sim.h5'.
 
-$ echo symgen P63 | pdbset xyzin model.pdb xyzout model-P1.pdb
+.SH REFLECTION LISTS
 
-While on this subject, you might also want to include hydrogens in the model
-using something like:
-$ echo HYDROGENS APPEND | hgen xyzin model.pdb xyzout model-with-H.pdb
+pattern_sim does not know about symmetry, so your input reflection list
+(give with "-i") must be expanded.  You can do this with:
+
+$ get_hkl -i myfile.hkl -o output.hkl -y mypointgroup -e 1
 
 Please be sure to read the "Note about Unit Cell Settings" in the documentation
 for indexamajig.