Content:
Here are some maybe more site-specific notes for the Data collection and structure determination in macromolecular crystallography course held in Aarhus in July 2018.
Our software is usually driven by commands within a terminal (shell) - although there is a task for running autoSHARP within the CCP4i (not CCP4i2). We recommend using that command-line interface, since it gives you full access to all features and tools of our software packages. Once you get used to this way of running programs it will become a very powerful way of running different programs (or different trials) on a large number of datasets.
You should be able to run jobs exactly as they are presented on the tutorial pages (for SHARP/autoSHARP or autoPROC) and described on the reference cards (autoSHARP, autoPROC) and in the manuals (SHARP/autoSHARP, autoPROC). Alternatively, Jesper (thank you!) has set up a SLURM command to run on a fast, high-performance cluster - e.g.
slurm_run run_autoSHARP.sh -seq 1o22.pir -ha "Se" -wvl 0.9778 peak -7 5 -sca 1o22_peak.sca -id 1o22_autoSHARP
You could run experimental phasing with the data you processed yesterday for the native plus Hg derivative dataset. Or have a look at the examples we provide here: just pick one of those examples - maybe one that will run quite quickly - and see what steps the program is performing. You could also pick just one of the various wavelength datasets for the MAD examples: some will work even with a single wavelength (SAD), while some might not work as well. Why is that?