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Serial Crystallography on I24
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
.
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
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
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
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 ssx: Pilatus 6M or Eiger CdTe 9M.
I - Align Jet
TBD
II - Set experiment parameters
-
Data collection set up
-
Pump Probe
TBD
IV - Run collection
TBD
I - Make coordinate system
Generally the first thing to do before running a chip collection is to set up the coordinate system.
- From the main edm screen open the
viewer
andmoveonclick
. - 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.
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
TBD
- 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
andShort2
: once opened set the laser dwell and delay times. -
Repeat#
: Set laser dwell and press calculate to get the delay times for eicah repeat mode.
TBD: get explanation from confluence
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.