My input star file for relion_refine seems good, it was written by relion_preprocess and looks the same as the star file I used to run your example : ribosomes wi/wo EFG (links to files in EMDB in the wiki are dead but in Google we can access).
The first lines of my input star file :
data_images
loop_
_rlnImageName #1
_rlnMicrographName #2
_rlnDefocusU #3
_rlnVoltage #4
_rlnSphericalAberration #5
_rlnAmplitudeContrast #6
[log in to unmask] 01 19999.540000 200.000000 2.000000 0.070000
[log in to unmask] 01 19999.540000 200.000000 2.000000 0.070000
I think problem appears in it000_model.star where, for each data_model_class#, _rlnSsnrMap #4 is "nan" as you can see :
data_model_class_1
loop_
_rlnSpectralIndex #1
_rlnResolution #2
_rlnAngstromResolution #3
_rlnSsnrMap #4
_rlnGoldStandardFsc #5
_rlnReferenceSigma2 #6
_rlnReferenceTau2 #7
0 0.000000 999.000000 nan 0.000000 0.000000 9.844030e-04
1 0.002149 465.407990 nan 0.000000 0.000000 0.036800
2 0.004297 232.703995 nan 0.000000 0.000000 0.095343
and all data_model_group# data blocks are empty.
How this snrMap value is calculated ? This is the problem or a consequence of the error?
Thanks
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