Differences

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--- relion [2024/08/29 07:09] – Luc Bonnefond
+++ relion [2024/08/29 07:12] (current) – Luc Bonnefond
@@ Line 19: / Line 19: @@
   * Manual picking/Display/Topaz : /shared/software/miniconda3-admin/envs/topaz-0.2.5/bin/topaz
-==== 1. Begin processing with relion ====
+==== Processing with relion ====
 Load and start relion (from cbi-compute-01 or the team GPU node (phantom-node39 for Lamour-Ruff))
@@ Line 35: / Line 35: @@
 <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
+  * <quote>--j</quote>: number of thread
-  * --max_frames: target number of frames to average (rounded to movies)
+  * <quote>--max_frames</quote>: target number of frames to average (rounded to movies)
-  * --random: randomize the order of input movies before taking subset
+  * <quote>--random</quote>: randomize the order of input movies before taking subset
 === Job Relion/Motion correction ===
@@ Line 53: / Line 53: @@
 <code>relion_display --i Micrograph.mrc --scale 0.2 --lowpass 10 --angpix 0.862 --sigma_contrast 3</code>
 Explanation of options:
-  * --i: Input; can be a single micrograph (.mrc) or a stack (.star), but not a movie (.eer, .tif)
+  * <quote>--i</quote>: Input; can be a single micrograph (.mrc) or a stack (.star), but not a movie (.eer, .tif)
-  * --scale: display size (0.2 = 20% of original)
+  * <quote>--scale</quote>: display size (0.2 = 20% of original)
-  * --lowpass: lowpass filtering (5 to 10 is a good range)
+  * <quote>--lowpass</quote>: lowpass filtering (5 to 10 is a good range)
-  * --angpix: angströms/pixel from the camera (0.862 for KriosI at x81000, 0.901 for KriosII and 0.729 for Glacios)
+  * <quote>--angpix</quote>: angströms/pixel from the camera (0.862 for KriosI at x81000, 0.901 for KriosII and 0.729 for Glacios)
-  * --sigma_contrast: contrast value to adjust (1 to 4, depending on the image, lowpass,...)
+  * <quote>--sigma_contrast</quote>: contrast value to adjust (1 to 4, depending on the image, lowpass,...)