Hi,
I set up 3 bodies in body-mask.star to run multi-body refinement. But during the running, I only see output files of 2 bodies rather than 3 bodies. Did I miss anything in settings? Thank you!
Jianhao
# Below are my body-mask.star and command.
$more ref/body-mask.star
data_
loop_
_rlnBodyMaskName
_rlnBodyRotateRelativeTo
_rlnBodySigmaAngles
_rlnBodySigmaOffset
_rlnBodyReferenceName
mask/body1.mrc 2 35 5 ref/body1.mrc
mask/body2.mrc 1 35 5 ref/body2.mrc
mask/body3.mrc 2 35 5 ref/body3.mrc
`which relion_refine_mpi` --continue MultiBody/job015/run_it010_optimiser.star --o MultiBody/job015/run_ct10 --reconstruct_subtracted_bodies --dont_combine_weights_via_disc --pool 60 --pad 2 --skip_gridding --j 5 --gpu "" --pipeline_control MultiBody/job015/
`which relion_flex_analyse` --PCA_orient --model MultiBody/job015/run_ct10_model.star --data MultiBody/job015/run_ct10_data.star --bodies ref/body-mask.star --o MultiBody/job015/analyse --do_maps --k 12 --select_eigenvalue 3 --select_eigenvalue_min -999 --select_eigenvalue_max 999 --pipeline_control MultiBody/job015/
$ ls MultiBody/job015/run_it*
MultiBody/job015/run_it009_data.star MultiBody/job015/run_it009_half2_model.star MultiBody/job015/run_it010_half2_body001.mrc
MultiBody/job015/run_it009_half1_body001_angdist.bild MultiBody/job015/run_it009_optimiser.star MultiBody/job015/run_it010_half2_body002_angdist.bild
MultiBody/job015/run_it009_half1_body001.mrc MultiBody/job015/run_it009_sampling.star MultiBody/job015/run_it010_half2_body002.mrc
MultiBody/job015/run_it009_half1_body002_angdist.bild MultiBody/job015/run_it010_data.star MultiBody/job015/run_it010_half2_model.star
MultiBody/job015/run_it009_half1_body002.mrc MultiBody/job015/run_it010_half1_body001_angdist.bild MultiBody/job015/run_it010_optimiser.star
MultiBody/job015/run_it009_half1_model.star MultiBody/job015/run_it010_half1_body001.mrc MultiBody/job015/run_it010_sampling.star
MultiBody/job015/run_it009_half2_body001_angdist.bild MultiBody/job015/run_it010_half1_body002_angdist.bild MultiBody/job015/run_it011_half1_body001_unfil.mrc
MultiBody/job015/run_it009_half2_body001.mrc MultiBody/job015/run_it010_half1_body002.mrc MultiBody/job015/run_it011_half1_body002_unfil.mrc
MultiBody/job015/run_it009_half2_body002_angdist.bild MultiBody/job015/run_it010_half1_model.star MultiBody/job015/run_it011_half2_body001_unfil.mrc
MultiBody/job015/run_it009_half2_body002.mrc MultiBody/job015/run_it010_half2_body001_angdist.bild MultiBody/job015/run_it011_half2_body002_unfil.mrc
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