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Hi Sjors, Thank you for your suggestion. That is exactly what the problem is. The coordinates were wrong when I extracted particles. I forgot about the binning issues. Thanks again, Chen ________________________________ From: Sjors Scheres <[log in to unmask]> Sent: Saturday, February 10, 2018 1:25:10 PM To: Chen Sun Cc: [log in to unmask] Subject: Re: [ccpem] relion 3D refine error Hi Chen, Have a look whether there are some empty or otherwise strange micrographs/particles in your data set. HTH, Sjors > Hi Joshua, > > > Thank you for your suggestion. I re-extracted particles with re-centering > but the refine 3D job still failed with the same error message. I don't > know what else I could try rather than reprocess from the beginning. > > > Sincerely, > > Chen > > ________________________________ > From: Collaborative Computational Project in Electron cryo-Microscopy > <[log in to unmask]> on behalf of Joshua Lobo <[log in to unmask]> > Sent: Friday, February 9, 2018 7:11:54 PM > To: [log in to unmask] > Subject: Re: [ccpem] relion 3D refine error > > Hi Chen > > Try extraction with re-center using the 2D classes from a previous > iteration that sometimes works > > Sincerely > Joshua Lobo > > On Feb 9, 2018 2:20 PM, "Chen Sun" > <[log in to unmask]<mailto:[log in to unmask]>> wrote: > > Dear List, > > > I encountered a strange problem in relion 3D refine step. It crashed > during the maximization of the first iteration. The error message is > presented below. > > > DIRECT_A1D_ELEM(sigma2, i)= nan > ERROR: > BackProjector::reconstruct: ERROR: unexpectedly small, yet non-zero sigma2 > value, this should not happen...a > > > I have never encountered this problem before but I found it in the Github. > It seems to be a bug of early versions of relion with the --always_cc > option. However, I am running on Relion/2.1.0 and I didn't specify > --always_cc. What may lead to this error? Is there anyone can help me out? > > > Here is the printed command: > > `which relion_refine_mpi` --o Refine3D/job125/run --auto_refine > --split_random_halves --i ./Extract/job121/particles.star --ref 360.mrc > --firstiter_cc --ini_high 60 --dont_combine_weights_via_disc --scratch_dir > /fast-cache/xdf --pool 3 --ctf --ctf_corrected_ref --particle_diameter 150 > --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 > --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym O > --low_resol_join_halves 40 --norm --scale --j 4 --gpu "2:3" > --dont_check_norm > > > > Many thanks, > > Chen > > -- Sjors Scheres MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44 (0)1223 267061 http://www2.mrc-lmb.cam.ac.uk/groups/scheres