We try to keep these notes for the CCP4/Shanghai (October 2019) workshop 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 or locally here. 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", "newest", "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).
  • You also get PDF reports named report.pdf (for the traditional, isotropic data analysis, i.e. truncate-unique.mtz) and report_startaniso.pdf for the anisotropically analysed data from STARANISO, staraniso_alldata-unique.mtz.

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 /home/ccp4admin/examples/mosflm/brazil -d autoPROC.01 | tee autoPROC.01.lis

In a second terminal, open the summary.html file via

cd ~/autoPROC
firefox autoPROC.01/summary.html

We will use this example during the practical tutorial - and then go through the output to show you the type of information provided by autoPROC processing with XDS, indication of possible problems,scaling, merging and anisotropy metrics.

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.

For data collected on Monday, 13th October 2019 at the SSRF beamlines (during this workshop), please remember that the rotation axis needs to be defined as rotating the reverse way by adding the parameter ReverseRotationAxis=yes, e.g.

     process ReverseRotationAxis=yes -I /where/ever/your/images -d autoPROC.01 > autoPROC.01.lis &
     firefox autoPROC.01/summary.html

If (a) the beamline/instrument you used for collecting your data is not listed, or (b) the instrumentation/setup has changed without us being aware of it and (c) 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.