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Streptavidin affinity grids (SAG) lattice subtraction

Requested files :

Place them all in a SAGsub3 folder in your home directory (~/SAGsub3/)

Most of the required python libraries are already available on the python hpc. Only the mrcfile library is missing and should be installed on phantom-node39 (I already did it, but I am not sure if its available for other account then mine)

ssh login@hpc.igbmc.fr
ssh login@phantom-node39
module load python/3.9
pip3 install mrcfile

Go to the folder containing the motion corrected micrographs to which the lattice subtraction needs to be applied (it can be resumed if it was partially ran before). Rub the command:

python3 ~/SAGsub3/SAGsub_3-2_stable_parallel_Nils.py --force_apix 0.729

The –force_apix 0.729 is for Krios2 datasets; it needs to be changed for the other microscopes/cameras

Useful commands:

Ctrl+Z to put the job in background
fg to bring the job to the foreground

You can check the results in the SAGsub.star file Format, with different columns:

Micrograph name
Mosaicity (should be 1 most of the time)
Discrepancy between simulated and optimized lattice (Ok up to a value of 1)
Success or fail (only tells you if the micrograph processing was done, regardless of the quality)