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:

  • the autoPROC command itself is called process
  • you need to tell the program where your images are (usually via the -I flag)
  • you want to save all output into a separate sub-directory - since you never know if you need/want to run processing multiple times to fine-tune or optimize it. It is useful to decide on a logical system for naming output directories consistently - e.g. 01, 02, 03 ... etc (and not "new", "newer", "newsest", "test", "test1" etc).
  • the main output/result file to look at (even while the job is running) is called summary.html and is located within the output sub-directory specified (you need to reload that file from time to time while the job is still running).

Example data

There are some local example datasets available at


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


process -I ~/Desktop/tutorials/dials/C2sum_1 -d example2 | tee example2.lis

and opening the summary.html file via

firefox ~/autoPROC/example1/summary.html


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.

Working with own data

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

  • rotation axis is inverted (relative to "standard" setup): add ReverseRotationAxis=yes to the command-line
  • rotation axis is vertical (instead of the more common horizontal orientation): add autoPROC_XdsKeyword_ROTATION_AXIS="0.0 -1.0 0.0" or autoPROC_XdsKeyword_ROTATION_AXIS="0.0 1.0 0.0"
  • beam-centre definitions as stored in image header follow unknown convention: you could try different conventions (e.g. BeamCentreFrom=header:y,x) or tell autoPROC to try and automatically test for it via BeamCentreFrom=getbeam:init

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.