The automated scripts run the programs XDS (data reduction, including integration and scaling), pointless (further space group determination), and aimless (final merging of data to produce the mtz you will need for structure solution). You can see the results directly within the b4 gui.

Pointless runs with default input and aimless uses the ONLYMERGE input. Aimless runs three times. For the first run, it produces the file aimless_all.log and aimless_all.mtz . As part of this run, it identifies the resolution cutoff based on cc(1/2)>0.3 and IsigI>2.0. It then runs again based on a resolution cutoff of cc(1/2)>0.3 and produces the files aimless_cc.log and aimless_cc.mtz . It then runs a final time based on IsigI>2.0, and produces the files aimless_IsigI.log and aimless_IsigI.mtz . Look for these files in the XDS folder which appears in your data directories. (Note that pointless and aimless only run when XDS has successfully produced the scaled file XDS_ASCII.HKL)

If processing went smoothly, you should see these files in your directory. You can use any of the mtz files for further structure solution:


We are now running an automatic data processing using xia2 to run DIALS. Similar to xds, it creates a DIALS subdirectory in the data collection directory where the images are. Look at xia2.html file for a nice table showing the processing results. If you open the xia2.html in a browser, you will see the results in a table like this:

Note that DIALS often takes up to half an hour after the last image was collected to finish, so you won’t see the directory appear right away.

Within the DIALS directory, you will see another directory called DataFiles. This contains the sca and mtz files resulting from processing.


Previously, we had automated scripts which processed data on 8.2.1 and 8.2.2 using Xia2, and the results were placed in the user home directory under the directory ~/rabbit_proc. We are no longer supporting these scripts, but you may still see some old processed data under this directory.

Thank you for reading!