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Serial Crystallography on I24

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Noemi Frisina edited this page Sep 19, 2023 · 36 revisions

General set up

Setting up the environment

To set up an enviroment to run the serial crystallography collection scripts, please follow the instructions here. Once this is done, the environment can be started by running:

cd /path/to/mx_bluesky
source .venv/bin/activate

On beamline I24, the package will be saved in /dls_sw/i24/software/bluesky.

Deploying a local version of the EDM screens

Every time a change is made to the template EDM screens saved in the repo, a new set should be deployed to the beamline ot to the dev environment to get the update. The deploy_edm_for_ssx.sh will create a local copy of the all EDM screens - both for a fixed target and for a serial jet collection - in a edm_serial/ directory with all the shell commands pointing to the correct scripts/edm locations.

./path/to/mx_bluesky/deploy/deploy_edm_for_ssx.sh

Setting the current visit directory

A new visit directory might need to be set before every user or commissioning beamtime. This can be done by a member of the beamline staff by modifying the file /dls_sw/i24/etc/ssx_current_visit.txt to point to the current visit and then running the command:

./path/to/mx_bluesky/src/mx_bluesky/I24/serial/set_visit_directory.sh

Note that the default experiment type for the script setting the directory will be fixed-target. In case of an extruder collection, to set the correct visit PV the experiment type should be modified from the command line.

./path/to/mx_bluesky/src/mx_bluesky/I24/serial/set_visit_directory.sh extruder

Running a collection

Starting the EDM screens

A couple of entry points have been set up so that:

  • run_fixed_target starts the edm screens for a fixed target collection
  • run_extruder starts the edm screens for a serial jet collection

Detector choice

The detector currently in use is automatically set by reading the position of the detector stage in the y direction. Detectors available for ssx: Pilatus 6M or Eiger CdTe 9M.

Extruder

TBD

Fixed-Target

I - Make coordinate system

Generally the first thing to do before running a chip collection is to set up the coordinate system.

  1. From the main edm screen open the viewer and moveonclick.
  2. Find the first fiducial in the top left corner, centre it and press set fiducial 0.
  3. Move to Fiducial 1 and 2 and repeat the process.
  4. Once all fiducials have been set, press make coordianates system. If all worked correctly it will find the first window in the first block.
  5. Run block check to check that all blocks are correctly aligned.

II - Select experiment parameters

In the edm screen fill the fields in Chip and Data Collation Setup with information such as sub-directory, filename, exposure time and detector distance.

IIa - Select chip and map type

TBD

IIb - Select pump probe

TBD Open Pump Probe screen from main edm. The box will appear by selecting one of the settings from the drop down menu. Once opened, set the laser dwell and delay times and press calculate to see set exp time set laser dwell and delay calculate sekect pp mode

III - Save the parameters

Before running a collection all parameters have to be saved using the Set parameters button. This step cannot be skipped! The parameters set in the previous step need to be saved so that they can be applied to the collection.

IV - Run a collection

Once all parameters have been set, press Start to run the collection. A stream log will show what is going on in the terminal.

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