Dear community,
I have a question about postprocessing step. For one specific dataset, 3D auto-refine gives me a density map without any noise. However, after mask creation on entire map and postprocessing, there are always huge amount of noise around structure. Can anyone please provide feedback how to avoid (or reduce) noise outside structure?
Thank you so much for the help!
This is the command of mask creation:
`which relion_mask_create` --i Refine3D/job403/run_ct7_class001.mrc --o MaskCreate/job410/mask.mrc --lowpass 15 --angpix 1.07 --ini_threshold 0.00286 --extend_inimask 1 --width_soft_edge 6 --j 3 (0.00286 is the threshold at which I can see each desired part of protein in chimera)
This is the command of postprocess:
`which relion_postprocess` --mask MaskCreate/job406/mask.mrc --i Refine3D/job403/run_ct7_half1_class001_unfil.mrc --o PostProcess/job410/postprocess --angpix 1.07 --mtf mtf_falcon2_300kV.star --auto_bfac --autob_lowres 10
Best wishes,
Da
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