Beta lactamase
This tutorial follows the same steps as this command line tutorial , but here processing will be driven graphically through the DIALS User Interface, Dui2.
The following example uses a Beta-lactamase dataset collected using beamline I04 at Diamond Light Source, and reprocessed especially for these tutorials.
[Hint:] If you are physically at Diamond on the CCP4 Workshop, then this data is already available in your training data area. After typing
module load ccp4-workshopyou'll be moved to a working folder, with the data already located in thetutorial-data/summedsub directory.
The data is otherwise available for download from here. We'll only be using the first run of data in this tutorial,C2sum_1.tar, extracted to a tutorial-data/summed subdirectory.
When DUI starts up you will initially be presented by a window like the following.
At this stage you can resize various parts of the interface until you are comfortable with the layout, but you can’t do much else until the dataset is imported by DIALS. To do this, click on the "Select file(s)" button, navigate to the location of the images and select any one of them. Dui2 will automatically determine the filename template and will show that with a wildcard in the text box. If there are problems with this template it is possible to edit this before importing the images. Otherwise, just click the “Run” button to proceed.
What happens then is that that the metadata are read for all the images in the dataset. If these are consistent, then the dataset is imported and initial models for the “Beam”, “Scan” and “Detector” are created. The images are now also displayed within the “Image” tab. You can adjust the contrast and colour scheme by controls under the “Display info ...” pull-down.
The first “real” task in any processing using DIALS is the spot finding. To run this job, click on the “find spots” button at the upper-left of the window. When you do this you will see a new node will be created in the “History Tree”. This node is currently green, which indicates that it has not been run yet. By contrast, the "Import" step is blue, which means this has been run. In general, it is always possible to navigate between each step of processing by clicking on the relevant position in the history. Advanced users will find this gives a great deal of control, allowing them to keep track of complex history, including parallel branches.
Spot-finding, like most of the other processing steps in Dui2, presents user parameters at two levels of detail. The “Simple” tab contains the basic parameters that are the most commonly changed. The “Advanced” tab contains all of those again, plus other parameters that may be required for expert use with challenging data sets. In many cases, however, the default settings are fine.
Note that spot-finding is done on every image in the dataset. This means the job can take some time, but by default it will be run in parallel using multiple processors. To proceed, press the “Run” button below the input parameters.
Once the job is finished, the image viewer will display small blue boxes around the pixels that have been marked as strong. It is also useful to click on the “Report” tab and scroll down to the “Analysis of strong reflections”. This shows a graph of the number of strong spots found per image. In this case there is a pretty steady rate of around 150 spots found on each image. If instead we had seen the number of strong spots drop off over the dataset, or otherwise show large variability we would start to worry about issues such as radiation damage or a poorly-centred crystal.