Exporting map and particle file to Relion 3.0



Hi all,
I am having some troubles with exporting my map and particle file from Cryosparc after refinement to Relion. Here is what I have been doing:

  1. Downloaded the J###.particles.alignments3D file and convert it to .star format using the command: csparc2star.py P1_J###_particles.cs cryosparc-particles.star

  2. Downloaded the J###.volume.map_half_A and changed the box size to match with the particle size using the command:
    relion_image_handler --i J###.volume.map_half_A.mrc --new_box 288 --o J###new-box288.mrc

  3. Now I am using cryosparc-particles.star and J###new-box288.mrc in Relion to run the refinement using the command:
    which relion_refine_mpi --o Refine3D/job039/run --auto_refine --split_random_halves --i Select/job034/particles.star --ref …/Downloads/job242-unfiltered.mrc --firstiter_cc --ini_high 60 --dont_combine_weights_via_disc --pool 3 --pad 2 --ctf --particle_diameter 208 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 3 --auto_local_healpix_order 3 --offset_range 5 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale --j 5 --gpu “”

The resulting map that I am getting in Relion is very poor and looks nothing like the map that I am getting from Cryosparc refinement. While cryosparc refines the map to 5.1A resolution and I see a lot of features especially all the helices, the map in Relion is about 17A and has absolutely no features at all.

I am concerned that I am doing something wrong in the process of exporting the files. Any suggestions in this regard would be very helpful please. Thanks.



The particle origins from cryoSPARC are in terms of the refinement box (not the particle box). Relion needs them in terms of the particle box.

You can use the --boxsize argument with csparc2star.py to fix this problem, by giving the refinement box (it will use the pixel size from the particles to make the correction).