Differences

This shows you the differences between two versions of the page.

--- titan_to_process [2024/02/02 15:32] – created Luc Bonnefond
+++ titan_to_process [2024/07/25 12:08] (current) – Luc Bonnefond
@@ Line 1: / Line 1: @@
 ====== Pre-processing of dataset from Titan II ======
+==== 1. Recover the dataset from the microscope ====
 Log into **cbi-gateway-01** to access the microscope and transfer the data to **gateway** or **storage**
@@ Line 6: / Line 8: @@
 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>
+rsync -avz --progress /mnt/titan2/offloaddata/TemScripting/EF-Falcon/<dataset> /mnt/storage/teams/<your_team_folder>/<project>/<dataset>
 </code>
-Path to gateway as seen from cbi-gateway-01 : <code>/mnt/zfspool/teams/</code>
+Path to gateway as seen from cbi-gateway-01 : <quote>/mnt/zfspool/teams/</quote>
-Log into **cbi-compute-01** and transfer the scripts <code>eer2tif_parallel_loop.py</code>, <code>eer2tif_parallel.py</code> and <code>eer2tif.py</code> in your **home**
+==== 2. Convert the EER movies to TIF ====
+Log into **cbi-compute-01** and transfer the scripts {{ ::eer2tif_parallel_loop.py |}} and {{ ::eer2tif_parallel.py |}} in your **home**
 <code>
 ssh <login>@cbi-compute-01
 module load relion
-cd /mnt/storage/teams/lamour-ruff/<project>/<dataset>/ #go to the folder with the dataset
+cd /mnt/storage/teams/<your_team_folder>/<project>/<dataset>/ #go to the folder with the dataset
 module load python
 python ~/eer2tif_parallel.py
 </code>
-Warning : conversion of eer to tiff file will show error this message : <code>TIFFReadDirectory: Warning, Unknown field with tag 65002 (0xfdea) encountered.</code>
+Warning : conversion of eer to tiff file will show error this message : <quote>TIFFReadDirectory: Warning, Unknown field with tag 65002 (0xfdea) encountered.</quote>
-# load relion and start relion
+==== 3. Begin processing with relion ====
+Load and start relion (from cbi-compute-01 or the team GPU node (phantom-node39 for Lamour-Ruff))
+<code>
+module load relion
 relion& #start relion in the folder with movies
+</code>
+=== Job Relion/Import ===
+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
-# Relion/Import *.tif , specify pixel size, voltage and run
+=== Estimation the camera gain ===
-# estimate the gain with at least 200 movies
+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 --o estimated_gain.mrc
+<code>relion_estimate_gain --i Import/job001/movies.star --j 8 --max_frames 10000 --random true --o estimated_gain.mrc</code>
+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
-# Relion/Motion correction , specify dose per frame, number of patches 5x5m, provide gain file, 20 threads
+=== Job Relion/Motion correction ===
+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)