CCP4 APS 2024

ccp4-aps-2024/TLDR.md

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+# TL;DR
+
+## Script
+
+This is the shortest script for processing the tutorial data with DIALS assuming you have the data in a parent directory:
+
+```
+dials.import ../Insulin_6_2.nxs
+dials.find_spots imported.expt
+dials.index imported.expt strong.refl
+dials.refine indexed.expt indexed.refl
+dials.integrate refined.expt refined.refl
+dials.symmetry integrated.expt integrated.refl
+dials.scale symmetrized.expt symmetrized.refl absorption_level=medium
+dials.export scaled.expt scaled.refl
+dials.merge scaled.expt scaled.refl
+```
+
+If you run this _before_ working through the tutorial you can spend the time playing with the viewers and looking at the log files (e.g. `less dials.index.log`) rather than waiting for the individual tasks to complete.

ccp4-aps-2024/image_viewer.md

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+# Image Viewer
+
+The DIALS image viewer can show a lot of useful diagnostic information: if you run with just the data i.e. `dials.image_viewer imported.expt` then you can walk through the steps of spot finding or look at the data / mask. If, however, you include the reflection data you can also look at the pixel classification from spot finding or the integration shoeboxes.
+
+## From Spot Finding
+
+If you run `dials.image_viewer imported.expt strong.refl` after `dials.find_spots` you can see:
+
+- the reflection bounding boxes (blue)
+- the "signal" pixels - marked with a green dot
+- the centre of mass of the spot (red cross)
+
+If you enable "show mask" you can also see those pixels which are excluded because (i) insensitive or (ii) already masked as they are known to be bad.
+
+## From Indexing
+
+If you have data from indexing then the bounding box will depend on the lattice number: for a multi-sweep experiment, or if you have multiple lattices on a single image set, you will see different colour boxes. You can also select "show HKL" to indicate the Miller indices, or "indexed only" to include only those spots which have been indexed. Looking at the results from refinement is essentially the same.
+
+## From Integration
+
+With the integration data you instead see the integration bounding boxes on the images, which are much larger as these include the background region. Frequently these will overlap with one another slightly if the spots become close together. If they overlap substantially there may be problems with these data e.g. a mosaic crystal or detector too close to the sample.
+
+[Return to main tutorial](./README.md)