Hi Sjors,
When I add additinal arguments --skip_align --no_map --use_all_data to relion_refine, the output result is identical to the reference. The FSC between them is 1. Even I use a small number of 3D particles (~50 particles) as input, the result is also the same as the reference. Anything wroing in my command line?
relion_refine --i Refine3D/job752/test_run_data.star --o Refine3D/job752/test/run4 --ref reference.mrc --ini_high 0 --dont_combine_weights_via_disc --pool 3 --ctf --ctf_corrected_ref --iter 0 --tau2_fudge 4 --particle_diameter 350 --K 1 --flatten_solvent --zero_mask --strict_highres_exp 10 --sym C1 --norm --scale --j 8 --angpix 4.34 --skip_align --no_map --use_all_data
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