Content:
Here are some maybe more site-specific notes for the SEA-COAST Workshop held at KMUTT/Bangkok in January 2020.
Remember to always run
module load ccp4 module load xds module load gphl
whenever you open a new terminal or open a new tab on an existing terminal.
As part of the lecture/demo/tutorials, we're going to first create a new directory to work in:
mkdir ~/autoSHARP cd ~/autoSHARP module load ccp4 module load xds module load gphl
We need the example data, namely:
(right mouse click, "Save file as") and move both files into the current directory:
mv ~/Downloads/1o22* .
Now we can start autoSHARP via
run_autoSHARP.sh -fast \ -seq 1o22.seq -ha Se \ -wvl 0.9778 peak -7 5 -sca 1o22_peak.sca \ -d 1o22.01 | tee 1o22.01.lis
and from a second terminal/tab open the results file with
firefox ~/autoSHARP/1o22.01/LISTautoSHARP.html
We will go through that result file as part of the tutorial in more detail: what is it telling us and what does it mean?
Our software is usually driven by commands within a terminal (shell) - although there is a task for running autoSHARP within the CCP4i (not CCP4i2) interface. 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 (which you should have as a print-out, see also autoSHARP, autoPROC) and in the manuals (SHARP/autoSHARP, autoPROC).
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?
If you pick one of those examples and download the relevant files (right mouse-click the file name/link and select "Save Link As..."), remember that they will be saved by default in your ~/Downloads folder. You might need to move them over to your current working directory with a command like
mv ~/Downloads/1o22* .
A good way of getting started is to run
run_autoSHARP.sh -h
to get a help message. At the end it will show some example commands for typical situations (SAD, MAD, SIRAS, partial model etc) that you should be able to easily adapt to your situation. Please note: