Pre-processing of dataset from Titan II

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/<your_team_folder>/<project>/<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 and eer2tif_parallel.py in your home

ssh <login>@cbi-compute-01
module load relion
cd /mnt/storage/teams/<your_team_folder>/<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 and start relion (from cbi-compute-01 or the team GPU node (phantom-node39 for Lamour-Ruff))

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

Give the path to the *.tif , specify the pixel size, voltage and hit RUN You can RESUME the job when more movies are transferred and converted

Estimate the gain with at least 200 movies (redo if needed with a larger number)

relion_estimate_gain --i Import/job001/movies.star --j 8 --max_frames 10000 --random true --o estimated_gain.mrc

Explanation of options:

• –j: number of thread
• –max_frames: target number of frames to average (rounded to movies)
• –random: randomize the order of input movies before taking subset

Specify the dose per frame, the number of patches 5x5m, provide the gain file, and set several MPI (number of tasks in parallel) and several (as a multiple of the number of frames in the movies) threads (number of cpu per task)