Content:
These are some notes for the SEA COAST 2019 workshop running at KMUTT (Bangkok) in January 2019. We will try and keep this up-to-date as we go along.
Remember, our software is usually run from the command-line (within a terminal). You should be reasonably familiar with some basic so-called shell commands - see e.g. also here.
To keep the different program and tutorial runs organised, it might be a good idea to run everything related to autoPROC in a separate directory, e.g. doing
mkdir ~/autoPROC cd ~/autoPROC
(the first command creates a sub-directory in your home directory and the second command changes your current working directory to that newly created one).
You should have a copy of the 2-sided autoPROC reference card in your handouts with the most commonly used command-line arguments. More details can be found in the online manual. The crucial bits to remember are:
There are some local example datasets available at
~/Desktop/tutorials
that can be used as examples for the different data processing tutorials during the workshop. After opening a terminal (click on the icon called "Terminal" on your desktop) you should be able to run autoPROC on these using e.g.
mkdir ~/autoPROC cd ~/autoPROC process -I ~/Desktop/tutorials/mosflm/images -d example1 | tee example1.lis
or
process -I ~/Desktop/tutorials/dials/C2sum_1 -d example2 | tee example2.lis
and opening the summary.html file via
firefox ~/autoPROC/example1/summary.html
or
firefox ~/autoPROC/example2/summary.html
We will use one of those examples during the practical tutorial - and then go through the output to show you the type of information provided by autoPROC processing with XDS.
This would not be fundamentally different to using the example/tutorial data mentioned above. Some additional care should be taken though - especially in checking for any beamline-specific settings. If the beamline/instrument you used for collecting your data is not listed or the instrumentation/setup has changed without us being aare of it and data processing is not working, the most common reasons (apart from poor diffraction quality) are
Have a close look at the information provided by the summary.html file, especially any warning messages that might point to problems with diffraction, crystal, instrumentation or processing.