Here are some maybe more site-specific notes for the CCP4/Shanghai Workshop held in October 2019.

Running jobs

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 (autoSHARP, autoPROC) and in the manuals (SHARP/autoSHARP, autoPROC).


For the tutorial we will use one additional settings that should not necessarily be used under normal conditions: it is only used to provide faster execution (so we have results to look at within the short amount of time available). This means setting the -fast flag: -fast ...

We are going to use some Se-MET MAD data for this tutorial: 3ISY. We have the following files:

Please download those files onto your computer: right mouse click and then "Save Link As...". This should save these 3 files into your ~/Downloads folder.

Next we want to create a directory via

    mkdir ~/autoSHARP

and go there:

    cd ~/autoSHARP

It is easiest to move the just downloaded files over here using

    mv ~/Downloads/3isy* .

Now we can decide what kind of phasing computation we want to do: the best one should be using 2-wavelength MAD. For this we are going to run \
        -fast \
        -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-1 | tee autoSHARP_MAD-1.lis

You could just cut-and-paste the above command into your terminal (mark with left mouse button, move into your terminal and press the middle mouse button, then hit return). Or type it at the prompt - in which case it would be all on one line without the "\" (continuation) characters.

When running, it will report something like

running autoSHARP (see /home/ccp4/autoSHARP/autoSHARP_MAD-1/LISTautoSHARP.html) ...

and you could open file:///home/ccp4/autoSHARP/autoSHARP_MAD-1/LISTautoSHARP.html) in your (firefox) browser. Remember to reload that page from time to time to refresh the content.

Once the jobs is finished, you could visualise results e.g. via

    cd autoSHARP_MAD-1/Results
    coot --script 05_coot.scm

Because we have 2 wavelength data here, we could also run SAD on one of the single wavelengths, e.g. \
        -fast \
        -seq 3isy.pir -ha "Se" \
        -wvl 0.97934 infl -11 3.3  -sca \
        -id autoSHARP_SAD-infl | tee autoSHARP_SAD-infl.lis

or \
        -fast \
        -seq 3isy.pir -ha "Se" \
        -wvl 0.91162 hrem -1.8 3.3 -sca \
        -id autoSHARP_SAD-hrem | tee autoSHARP_SAD-hrem.lis

It might actually be interesting to see how these different approaches behave in terms of phasing: which of the two wavelengths works on its own (as SAD)? Does 2-wavekength MAD give us better experimental phasing as expected?

You could now re-run these examples without the -fast flag: this would produce more - probably interesting - analysis and possibly a better (e.g. more complete) inital model. Please remember to change the output identifiers in this case (argument to the -id flag and the file name given after tee).


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 them over to your current working directory with a command like

mv ~/Downloads/1o22* .

A good way of getting started is to run -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:

When working with your own data, please remember: