Import single-particle data in star format


  • Star file from 3D classification or refinement jobs (*

  • Star file with motion correction results (MotionCor/{job_id}/

  • Absolute path to the corresponding Relion project folder


A single command is needed to convert the project to the pyp format:

rlp -import_read_star -import_refine_star "path_to_refinement_star_file" -import_relion_path "RELION_project_path" -import_motion_star "" -scope_pixel pixel_size -scope_voltage voltage -data_path path_to_raw_movies -data_mode "spr" -import_mode "SPA_STAR"

After running this command, everything necessary to continue refinement in pyp will be created.

Export single-particle data in star format

Export data from pyp

  • Go to the pyp project directory and run:

csp -export_enable                              \
    -export_parfile "path_to_parfile"           \
    -export_location "path_to_export_location"

A star file will be saved in the export_location folder with a basename corresponding to the dataset name.

  • Import the project into Relion

    1. Start a new Relion project:

    cd relion/
    # create links tp pyp frame averages into Micrographs folder
    mkdir Micrographs
    cd Micrographs
    ln -s {pyp_project_path}/ali/*.mrc .  # link the *_DW.mrc files if you want to use dose-weighted averages
    cd ..
    # start Relion
    relion &
    1. If not doing movie correction in Relion, import micrographs using the star file converted from PYP

    2. Re-extract particles in Relion (either re-center based on the particles shifts or not)

    3. Do refinement or classification with the re-extracted particles


If you want to use Relion’s motion correction results, you will need to import the raw movies instead of the frame averages. The _rlnMicrographName column in the star file converted from pyp is in the following format: Micrographs/{image_name}.mrc

Bfore importing the raw movies into Relion, we need to edit the _rlnMicrographName column as follows:

sed -i 's/Micrographs/MotionCor\/{job_id}\/{where_the_aligned_images_saved}/g' {dataset_name}.star


If there are . characters in the micrograph names, Relion will substitute them by _. In this case, you can use a similar sed command to edit the star file before importing the data.