Slide 25 of 27
It’s probably easiest to check through the different log files produced by SCALA with the ccp4i GUI.
- The ROGUES file contains a list of the reflections which have been rejected because the symmetry equivalents differ considerably, and also those reflections with Emin too large. It is probably worthwhile trying to work out why the reflections are there! A common reason is that one equivalent is partly hidden behind the backstop arm, so has an anomalously low intensity.
- The Normal Probability Plot is useful for determining if the data have a reasonable distribution of intensities; the bulk of the points should lie on the diagonal with slope = 1, for both fully recorded reflections and partials. If there is considerable thermal diffuse scattering, the “partials” graph will be well above that of the “fulls”, indicating a negative partial bias. This may be addressed by using the “TAILS” option, which makes a reasonable attempt to correct for this effect.
- The Surface Plot (produced only when a secondary beam correction is applied) is useful for determining whether or not an absorption correction is necessary; large deviations from the flat graph indicate that this might be so.
- The full SCALA log file, much like the mosflm.lp file, probably contains more information than will be used. Most people will be interested in Rmeas (i.e. multiplicity weighted Rmerg), completeness and resolution figures, but it’s well worthwhile spending more than a couple of minutes checking the file.