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--- sagsub [2024/02/22 10:36] – created Luc Bonnefond
+++ sagsub [2024/08/29 06:56] (current) – Luc Bonnefond
@@ Line 1: / Line 1: @@
 ====== Streptavidin affinity grids (SAG) lattice subtraction ======
+Requested files :
+  * {{ :gridtools.py |}}
+  * {{ :mrc_rw_3.py |}}
+  * {{ :pattern_optimizer.py |}}
+  * {{ :sagsub_3-2_stable_parallel_nils.py |}}
+Log onto the Lamour GPU node:
+<code>
+ssh my_login@hpc.igbmc.fr
+ssh my_login@phantom-node39
+</code>
+Place the 4 python scripts in a SAGsub3 folder in your hpc home directory (<quote>~/SAGsub3/</quote>)
+Most of the required python libraries are already available on the python module available on the igbmc 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)
+<code>
+ssh my_login@hpc.igbmc.fr
+ssh my_login@phantom-node39
+module load python/3.9
+pip3 install mrcfile
+</code>
+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).
+From the igbmc hpc, the storage path is : <quote>/shared/misc/cbi-teams/</quote>
+Run the command:
+<code>
+python3 ~/SAGsub3/sagsub_3-2_stable_parallel_nils.py --force_apix 0.729
+</code>
+The <quote>--force_apix 0.729</quote> is for Krios2 datasets; it needs to be changed for the other microscopes/cameras (0.862 for Krios1 and 0.901 for Glacios)
+Useful commands:
+  * Ctrl+Z to put the job in background
+  * <quote>fg</quote> to bring the job to the foreground
+You can check the results in the <quote>SAGsub.star</quote> file, formatted 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)