Log into cbi-gateway-01 to access the microscope and transfer the data to gateway or storage

ssh <login>@cbi-gateway-01
ls /mnt/titan2/offloaddata/TemScripting/EF-Falcon/<dataset>
rsync -avz --progress /mnt/titan2/offloaddata/TemScripting/EF-Falcon/<dataset> /mnt/storage/teams/lamour-ruff/Top2-G4/<dataset>

Path to gateway as seen from cbi-gateway-01 :

/mnt/zfspool/teams/

Log into cbi-compute-01 and transfer the scripts

eer2tif_parallel_loop.py

,

eer2tif_parallel.py

and

eer2tif.py

in your home

ssh <login>@cbi-compute-01
module load relion
cd /mnt/storage/teams/lamour-ruff/<project>/<dataset>/ #go to the folder with the dataset
module load python
python ~/eer2tif_parallel.py

Warning : conversion of eer to tiff file will show error this message :

TIFFReadDirectory: Warning, Unknown field with tag 65002 (0xfdea) encountered.

# load relion and start relion relion& #start relion in the folder with movies

# Relion/Import *.tif , specify pixel size, voltage and run

# estimate the gain with at least 200 movies relion_estimate_gain –i Import/job001/movies.star –j 8 –o estimated_gain.mrc

# Relion/Motion correction , specify dose per frame, number of patches 5x5m, provide gain file, 20 threads