Beamline Phone Number:
+44 (0) 1235 778418
Principal Beamline Scientist:
Dave Allan
Tel: +44 (0) 1235 778644
E-mail: [email protected]
Email: [email protected]
Tel: +44 (0)1235 4494052
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:
Action |
xia2 Instruction |
Include space group and unit cell (both must be used together) |
space_group= unit_cell=“a b c α β γ” OR unit_cell=a,b,c,α,β,γ |
Maximum resolution cutoff |
d_min= |
Choose a different indexing method |
index.method= index.method=real_space_grid_search (normally the most robust method) |
Set a threshold so only the strongest reflections are used for indexing |
sigma_strong= (default value is 3) |
absorption correction |
absorption_level= choose from low/medium/high as most appropriate |
Select which images should be included, for example to omit images which look to have radiation damage |
image=path/to/images/image_XX_00001.cbf:first:last OR copy over an automatic.info file produced for the same dataset and edit the images required in this file - save as edit.info include xinfo=edit.xinfo |
Can help integration complete |
scan_varying=false |
If beam centre refinement is unstable | trust_beam_centre=True |
Will make the job complete even if the processing doesn’t work for all sweeps |
failover=true |
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.
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