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.\"
.\" pattern_sim man page
.\"
.\" Copyright © 2012 Thomas White <taw@physics.org>
.\"
.\" Part of CrystFEL - crystallography with a FEL
.\"
.TH PATTERN\_SIM 1
.SH NAME
pattern\_sim \- Simulation of nanocrystal diffraction patterns
.SH SYNOPSIS
.PP
.B pattern\_sim
[options]
.SH DESCRIPTION
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:
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.
The result will be written to an HDF5 file in the current directory with the name `sim.h5'.
.SH REFLECTION LISTS
You'll need to create a file containing the intensities of the reflections. The normal way to do this is to use CCP4 via the "gen-sfs" script in CrystFEL's script folder. Run it like this:
$ gen-sfs mymodel.pdb "P6" 3
You need to give the PDB model, the symmetry of the output reflections (use the lowest symmetry space group with the right point group), and optionally the maximum resolution in Angstroms. If you don't specify the resolution, it'll use 3 Angstroms.
The reflections will be output as "mymodel.pdb.hkl" ready for input to pattern_sim. You'll need to give the Laue class of the symmetry you gave to gen-sfs, "6/m" in this case, to pattern_sim with the "-y" option. By default, gen-sfs calculates the values for CuKa radiation (8.3 keV, 1.5 A). It will not calculate the anomalous contribution to scattering, i.e. the differences in intensities between Bijoet pairs. Both of these are the default behaviour for "sfall" in CCP4, so read the manual for that for further details. If you need something different, get the "ano_sfall.com" script from James Holton and turn the output into a CrystFEL reflection list in a similar way.
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