Hi Sjors,
I tried to re-refine the polished particles.
However, I got these error messages.
ERROR: It appears that these images have not been normalised to an average background value of 0 and a stddev value of 1.
Note that the average and stddev values for the background are calculated outside a circle with the particle diameter
You can use the relion_preprocess program to normalise your images.
If you are sure you have normalised the images correctly (also see the RELION Wiki),
you can switch off this error message using the --dont_check_norm command line option
File: src/ml_optimiser.cpp line: 1186
in the .err log file, there are some lines (I only see part of them)
fn_img= [log in to unmask] bg_avg= -4.3864e-10 bg_stddev= 5
fn_img= [log in to unmask] bg_avg= 6.40517e-10 bg_stddev= 5
fn_img= [log in to unmask] bg_avg= 8.88438e-10 bg_stddev= 5
fn_img= [log in to unmask] bg_avg= -1.4648e-09 bg_stddev= 5
fn_img= [log in to unmask] bg_avg= 9.57298e-10 bg_stddev= 5
..
..
..
I don't have this problem in 2D, 3D classification or refinement.
The particle extraction with movie finished without errors.
Also, the particle polishing procedure finished without errors.
Is there a way I could just normalize these particle images to solve the problem?
Or should I use --dont_check_norm? or delete these particles?
Thank you.
Chia
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