BSI wiki

Log in on the igbmc HPC or the team GPU

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

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

Load and start relion (from cbi-compute-01 or the team GPU node (phantom-node39 for Lamour-Ruff))

relion& #start relion in the folder with movies

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

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 --max_frames 10000 --random true --o estimated_gain.mrc

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

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)

Open a window to select the display parameters of a micrograph:

relion_display --i Micrograph.mrc --gui

Or

Specifity the parameters for display in the command:

relion_display --i Micrograph.mrc --scale 0.2 --lowpass 10 --angpix 0.862 --sigma_contrast 3

Explanation of options:

• –i: 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)
• –lowpass: 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)
• –sigma_contrast: contrast value to adjust (1 to 4, depending on the image, lowpass,…)