Serial Crystallography on I24

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

Before opening the experiment specific edm, each of these entry points will start a BlueAPI server.

Detector choice

The detector currently in use is identified by reading the position of the detector stage in the y direction. A different detector can be chose by opening the Detector tab in the main edm screen, selecting the detector name from the list and clicking the Move Stage button, which will move the detector stage to the correct height and update the relative PVs.

Detectors available for serial: Pilatus 6M or Eiger CdTe 9M.

Extruder (Serial Jet)

On startup, once both the visit and the detector have been set up, always press the initialise on start button, which will autofill the general purpose PVs for an extruder collection with sensible default values, as well as the chosen visit directory and detector. Ensure that the visit shown on the edm screen is correct.

I - Align Jet

Open the viewer and switch on the backlight to visualise the jet stream. You can use the positioners in the Align Jet panel on the edm screen to move the orizontal goniometer table and align the jet.

II - Set experiment parameters

Data collection set up

TBD

Pump Probe

TBD

WARNING This setting required an hardware change, as there are only 4 outputs on the zebra and they are all in use. When using the Eiger the Pilatus trigger cable should be used to trigger the light source. When using the pilatus the eiger trigger cable should be used.

III - Run 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.

Fixed-Target (Serial Fixed)

I - Make coordinate system

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

Before this step remember to reset the scale and skew factors as well as the motor directions as needed. Current values are saved in src/mx_bluesky/I24/serial/parameters/fixed_target in the cs_maker.json and motor_direction.txt files.

From the main edm screen open the viewer and moveonclick.
Find the first fiducial in the top left corner, centre it and press set fiducial 0.
Move to Fiducial 1 and 2 and repeat the process.
Once all fiducials have been set, press make coordianates system. If all worked correctly it will find the first window in the first block.
Run block check to check that all blocks are correctly aligned. WARNING: block check is not available for a custom chip.

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.
Select chip and map type

Select the Chip Type from the drop-down menu on the edm screen, and if using a non-custom chip also select Map Type.

For a full-chip collection on an Oxford-type chip, Map Type should simply be set to None.
For a Custom Chip, click on the Custom Chip button, which will bring up the relative edm. Here, the steps are the following:
1. Clear Coordinate System. This will reset the coordinates.
2. Fill in the fields for number of windows and step size in x/y direction.
3. Press Set current position as start.
4. Once finished, close and return to main screen.
For collecting only on specific windows on an Oxford chip:
1. Set the Mapping Type to Lite. This will make the Lite launchers button visible.
2. On the launcher, select the blocks to collect - either manually or using a preset set.
3. Run Save Screen Map. This will create a currentchip.map file which will be copied to the data directory at collection time.
4. Run Upload Parameters.
5. Once finished, close and return to main screen.

Select pump probe

After setting the exposure time, open Pump Probe screen from main edm. The box will appear by selecting one of the settings from the drop down menu.

Short1 and Short2: once opened set the laser dwell and delay times.
Repeat#: Set laser dwell and press calculate to get the delay times for each repeat mode.
Medium1: open and close fast shutter between exposures, long delays between each one.

Select the most appropriate pump probe setting for your collection and set the laser dwell and delay times accordingly.

For more details on the pump probe settings see Dynamics and fixed targets

III - Save the parameters

This step cannot be skipped!

Once all of the previous steps have been completed - and before running a collection - all parameters have to be saved using the Set parameters button so that they can be applied to the collection. A copy parameter file will be saved along with the chip map (if applicable) in the data directory at collection time.

IV - Run a collection