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Table of Contents
Pre-processing of dataset from Titan II
Recover the dataset from the microscope
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/
Convert the EER movies to TIF
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.
Begin processing with relion
Load and start relion (from cbi-compute-01 of phantom-node39)
module load relion relion& #start relion in the folder with movies
Job Relion/Import
Give the path to the *.tif , specify the pixel size, voltage and hit RUN You can REMUSE the job when more movies are transferred and converted
Estimation the camera gain
Estimate the gain with at least 200 movies (redo if needed with a lager number
relion_estimate_gain --i Import/job001/movies.star --j 8 --o estimated_gain.mrc
Job Relion/Motion correction
Specify the dose per frame, the number of patches 5x5m, provide the gain file, and set 20 threads