===== Relion =====

Log in on the igbmc HPC or the team GPU

<code>
ssh -X login@hpc.igbmc.fr

ssh -X login@phantom-node39 #GPU node for lamour-ruff team

module load relion/4.0.0

module load ctffind/4.1.13

module load topaz/0.2.5
</code>

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

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,...)