Reprocessing

It is possible to reprocess the data with xia2 from within ISPyB with some (but not all) additional instructions.  These jobs are run in addition to the auto processing.

From the Data Collections page, first click on the entry next to Group to access all sweeps for that data collection, and then click on the cog for the first run you want to include to open the reprocessing window.

Now click on the cog wheels for any other sweeps of data to be included – these will be added to the list in the Reprocess Data window.

By opening the sweeps in reverse order, e.g., 4,3,2,1, the results will be included with the top run, i.e., run 4 which allows for easier comparison with the auto processing results (for all 4 sweeps).

It is necessary to select which images are to be included from each sweep – either highlight (from left to right) on the plot or type the image numbers in the boxes. Clicking on the + button will autofill with the entire sweep.

Process Individually should be left unchecked

Xia2-dials is the best pipeline but if it isn’t working, the others can be tried

The high resolution limit can be set in the High Res box, probably based on inspection of the auto processing results (see xia2.txt and merging-statistics.txt).

Clicking on the Space Group/Cell button opens the option to input the known or expected information.

The Options button has one check box for small molecule – this is checked by default for I19 data and should be left checked unless you are sure you know better.

At the bottom of the Reprocess Data window click on the Integrate button and a red message box should pop-up to show the job has been successfully submitted.

Navigate to the Reprocessing window to check the job is progressing and see when it has completed.

The Reprocessing window is accessed from the line of option buttons and shows a list of current and completed reprocessing jobs with any input commands set, i.e., resolution, unit cell information and which images were used.  Click on the relevant line (the top line has the results for all included sweeps) under Files to be taken to the results of the processing job.

This will appear as another result in the Auto Processing section for that data collection.  Theindicates that this is a manually started reprocessing job rather than an auto processing job.  At this point, all functions for the reprocessed job match those of the auto processing.