Command Line

For more information about running DIALS, check the website: DIALS: Diffraction Integration for Advanced Light Sources — DIALS documentationl

Reprocessing jobs using xia2 / DIALS can be submitted directly using the command line.

The first step is to navigate to the processing directory within the visit folder as this is the only place with write access.

Open a terminal window and, if not already done, type module load i19 and press enter.

This should direct you to your current visit directory, e.g.: /dls/i19-1/data/2024/cm37266-1 as well as enable DIALS to work.

Now type: cd processing

Create a suitably named directory for the processing files to be written in, e.g.: mkdir SampleA

And then enter the directory: cd SampleA

Use of DIALS to run processing step-by-step is not covered here, but there is an example of how to do it here: Small-molecule data reduction tutorial — DIALS documentation

Useful things to know:

The up arrow
     Press this once to redo the command above
     Repeated pressing will scroll through previous commands (to save quite a lot of tedious typing)

TAB key
     If enough information is already included, TAB will autocomplete instructions (saving tedious typing)
     Double TAB will give the options available from whatever is input

Copy and Paste must be done via the right mouse button

Everything is case sensitive

The easiest way to invoke a DIALS processing job is to run xia2, as all of the steps are run sequentially automatically.

The basic xia2 command is:
xia2 small_moleule=true /dls/i19-1/data/2024/cm37266-1/SampleA

where:
xia2 – runs a xia2 processing job
small_moleule=true – tells DIALS to run a small molecule processing job, which means things like cell errors are calculated
/dls/i19-1/data/2024/cm37266-1/SampleA – path to where the images are stored.

Various additional instructions can now be added to this command – see the table below for some of the most common ones:

So, an example command may look like:
xia2 small_moleule=true sigma_strong=15 index.method=real_space_grid_search space_group=P21 unit_cell=“7.72 8.68 10.82 90 103 90” /dls/i19-1/data/2024/cm37266-1/SampleA

Manually running xia2 processing does not include the structure solution step.

You can now export the shelxt.ins and shelxt.hkl files for structure soloution or, if desired, shelxt can be run on the xia2 output files here.

Navigate to where the files are: cd DataFiles
To run shelxt, type: shelxt shelxt

It is possible to include the correct (expected) atom types by editing the atom types listed in the shelxt.ins file using gedit shelxt.ins

The manual xia2 processing results are not incorporated into ISPyB so must be viewed (use gedit to open files from the terminal) within the file system – useful files can be found in the following locations.

Main folder:
     xia2.txt
     xia2.html

DataFiles subdirectory:
     Shelxt.ins and shelxt.hkl, plus any output files from running shelxt
     Xia2.cif

LogFiles subdirectory:
     AUTOMATIC_DEFAULT_NATIVE_merging-statistics.txt

The file structure is slightly different for data reprocessed manually using the command line - the files from spot finding and indexing are located within DEFAULT\NATIVE\SWEEP1\index.

If you are concerned about radiation damage and want to check for evidence, there is a damage analysis tool.  From the directory xia2 was started from type:
dials.damage_analysis DataFiles/AUTOMATIC_DEFAULT_scaled.{expt,refl}
     (shortcut type: dials.dam TAB)

Then open the resulting file by typing:
firefox dials.damage_analysis.html &

Look at the Rcp vs dose plot to check where the line veers off and then use this as a guide as to where to cut the data for the next reprocessing job.

It is possible to use pairs of .expt and .refl files in the dials reciprocal space viewer and image viewer in the same way as for the auto processed results.