I am using EMAN2 for particle processing and transferring data into relion for further refinement. The error came up when I did 2D classification after data transferred into relion format. In class.mrc files, only one out of my 40 classes is showing something and all other 39 images are pure black. This problems happened every time no matter whether my input had been ctf corrected or not. Usually, the first few iterations were good, but after around 5th iteration, images started to miss and in the end, only one would still be there.
Here is the command I used:
relion_refine --i all_images.star --o relion2d_04/run01/relion2d_04 --angpix 2.7 --K 40 --ctf_phase_flipped --iter 10 --tau2_fudge 1.0 --particle_diameter 50.0 --zero_mask --psi_step 15.0 --offset_range 6.0 --offset_step 2.0 --j 20 --dont_check_norm
What is the problem and how can I fix it?
Thanks so much.