Shell Scripts

There are a number of shell scripts included in Topaz3.

They mainly serve as an interface to command line tools provided by CCP4.

However, they are most likely specific to use at Diamond and will therefore require alterations to work properly on other machines.

Let’s take a look at topaz3/shell_scripts/cfft.sh:

#!/bin/bash

module load ccp4

cfft "$@"

This script does nothing other than load a specific module and call cfft with the parameters that are passed into it.

If cfft is installed directly on your machine, or is available through a different evironment, change the “module load …” line so that it works for you. This may involve simply removing it.

It should be possible to test that this is working by running:

topaz3/shell_scripts/cfft.sh --help

which should connect to your installation of cfft and show the help information.

This shell script should now work properly within the data transformation pipeline.

Simply repeat this process for the other shell scripts.