If you haven't brought your own datasets, there are enough example datasets available (see below). It might be good to

  • create a separate directory for this tutorial, e.g.
      mkdir -p ~/autoSHARP
  • go to this directory (of course, you can chose a different directory name and location if you want):
      cd ~/autoSHARP -h

Example datasets and tutorials

There are several examples and tutorials available, e.g.

  • some suggested runs could be (to be faster - depending on the speed of the computing hardware at the course - just add the flag "-fast" to the command line: those jobs should still work fine with this):
          % -seq 1o22.pir -ha "Se" \
                             -wvl 0.9778 peak -7 5 -sca \
                             -id autoSHARP_SAD | tee autoSHARP_SAD.lis
          % -seq 3isy.pir -ha "Se" \
                             -wvl 0.97934 infl -11 3.3  -sca \
                             -wvl 0.91162 hrem -1.8 3.3 -sca \
                            -id autoSHARP_MAD | tee autoSHARP_MAD.lis
    • MIRAS: 3ZFT.pir (this can run for a bit longer, but when running with the -fast switch it is possible the refined phases are not good enough for interpretation of density)
          % -seq 3ZFT.pir \
                             -nat -sca \
                             -ha "Hg" -nsit 1 -wvl 1.54179 -sca \
                             -ha "Ir" -nsit 2 -wvl 1.54179 -sca \
                             -id autoSHARP_MIRAS | tee autoSHARP_MIRAS.lis
  • or use your own data, especially if you have
    • a sequence file (see here for format description)
    • a reflection file (merged MTZ or *.sca)
    • information about heavy atom(s) (number, f'/f'' etc)