Differences

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--- relion [2023/11/02 08:23] – created Luc Bonnefond
+++ relion [2024/08/29 07:12] (current) – Luc Bonnefond
@@ Line 1: / Line 1: @@
 ===== Relion =====
+Log in on the igbmc HPC or the team GPU
 <code>
 ssh -X login@hpc.igbmc.fr
-ssh -X login@phantom-node39
+ssh -X login@phantom-node39 #GPU node for lamour-ruff team
 module load relion/4.0.0
@@ Line 13: / Line 15: @@
 </code>
-CTF estimation/CTFFIND-4.1/CTFFIND-4.1 executable : /shared/software/ctffind/4.1.13/bin/ctffind
+Executable location:
+  * CTF estimation/CTFFIND-4.1/CTFFIND-4.1 : /shared/software/ctffind/4.1.13/bin/ctffind
+  * Manual picking/Display/Topaz : /shared/software/miniconda3-admin/envs/topaz-0.2.5/bin/topaz
+==== Processing with relion ====
+Load and start relion (from cbi-compute-01 or the team GPU node (phantom-node39 for Lamour-Ruff))
+<code>
+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
+=== Estimation the camera gain ===
+Estimate the gain with at least 200 movies (redo if needed with a larger number)
+<code>relion_estimate_gain --i Import/job001/movies.star --j 8 --max_frames 10000 --random true --o estimated_gain.mrc</code>
+Explanation of options:
+  * <quote>--j</quote>: number of thread
+  * <quote>--max_frames</quote>: target number of frames to average (rounded to movies)
+  * <quote>--random</quote>: randomize the order of input movies before taking subset
+=== 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)
+=== Display micrographs for visual inspection ===
+Open a window to select the display parameters of a micrograph:
+<code>relion_display --i Micrograph.mrc --gui</code>
+Or
-Manual picking/Display/Topaz executable : /shared/software/miniconda3-admin/envs/topaz-0.2.5/bin/topaz
+Specifity the parameters for display in the command:
+<code>relion_display --i Micrograph.mrc --scale 0.2 --lowpass 10 --angpix 0.862 --sigma_contrast 3</code>
+Explanation of options:
+  * <quote>--i</quote>: Input; can be a single micrograph (.mrc) or a stack (.star), but not a movie (.eer, .tif)
+  * <quote>--scale</quote>: display size (0.2 = 20% of original)
+  * <quote>--lowpass</quote>: lowpass filtering (5 to 10 is a good range)
+  * <quote>--angpix</quote>: angströms/pixel from the camera (0.862 for KriosI at x81000, 0.901 for KriosII and 0.729 for Glacios)
+  * <quote>--sigma_contrast</quote>: contrast value to adjust (1 to 4, depending on the image, lowpass,...)