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



The symmetry of the molecular model (the space group)
-----------------------------------------------------

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:

$ echo symgen P63 | pdbset xyzin model.pdb xyzout model-P1.pdb

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


A Note about Unit Cell Settings
-------------------------------

Please be sure to read the "Note about Unit Cell Settings" in the documentation
for indexamajig.