Exporting map and particle file to Relion 3.0

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#1

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.

-Sadeem


#2

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).