Pages for the different workshop sections:

Follow-up tutorials:


These tutorials use the images and information made available for the Data Processing With The Pros session 08.15 at the ACA 2011 meeting in New Orleans. The datasets should be available for users to download, so that anyone should be able to process them in the same way as described in these pages here.

Unless specified, we assume that

  • the latest version of autoPROC (currently 1.0.0) is installed
  • CCP4 is installed and setup (these tutorials were run with a pre-release version ov CCP4 6.2.0)
  • XDS is installed (we used the "December 6, 2010" version)
  • 'gnuplot' is available on your system (to generate some graphs and plots)

We're going to use 'display' (from the ImageMagick package) to display PNG images and 'adxv' (from here) to look at diffraction images.

We will run all examples in a directory with the images for the given dataset present.

Scope and idea behind these tutorials

We want to show three things here:

  1. how to run autoPROC as easy as possible on a given set of images
  2. how to interpret the output and results from autoPROC
  3. how to potentially improve the results through some advanced features of autoPROC

One caveat: processing data that you didn't collect yourself is always error-prone. Most information about the crystal, how it was treated before or during the experiment, what happened during the data collection and how the data was actually collected (several crystals, same crystal, translated crystal) etc is all lost. So some of the assumptions you'll see throughout these tutorials might be completely wrong - but without further details it is difficult to explain all features visible in those example images.

References, 3rd-party software and acknowledgments

The main reference for autoPROC is:

Vonrhein, C., Flensburg, C., Keller, P., Sharff, A., Smart, O.,
Paciorek, W., Womack, T. & Bricogne, G. (2011).Data processing and
analysis with the autoPROC toolbox. Acta Cryst. D67, 293-302.

The paper is available as open access in HTML or as PDF.

Furthermore, autoPROC and this tutorial make use of the following 3rd-party software:

We want to acknowledge the generous support (as well as very valuable feedback and supply of test data) by the Global Phasing consortium. autoPROC has also seen support by the EU BIOXHIT project (LSHG-CT-2003-503420). The JCSG repository of datasets has been very helpful in testing the program. Developers of external software, detector manufacturers and beamline scientists have always been very helpful in answering questions or providing test data.

Some additional tools

Here are some additional tools/scripts that might come in handy: if you place them somewhere into your PATH, they will be picked up in the same way as described in the tutorials.

  • extracts data collection timestamp from a series of images and (optionally) sorts the output by date. This can be very handy when trying to do a post-mortem analysis of datasets you haven't collected yourself.
  • very trivial script to show beam centre values for all 8 poissible coordinate conventions.