Hi Leo,
The masking will not generate these artefacts. They are already present 
in your refined map (albeit perhaps less visible prior to the 
sharpening). It could be that the helical symmetry isn't correct, or it 
could be that some floppy densities are sticking inside the helix. Does 
the rest of the subunit show good 4.2A protein-like features, or is 
everything a bit weird? The latter seems the case (from your pdf), which 
may indicate helical symmetry isn't quite right yet. I also don't really 
like the shape of your FSC curve.... But ultimately these things are 
hard to tell from a distance.
HTH,
Sjors

On 12/07/2016 04:51 PM, Kong, Leopold (NIH/NIDDK) [F] wrote:
> Hi,
>
> I've been using helical processing in relion for a dataset.  After 3D auto refine, I got a map (upper right corner, purple), that seems reasonable to be ~ 6 Angstrom.  Relion estimated it to be ~ 4.4 Angstrom.  I did post processing with a mask (right for FSC curves of pre and post processing), which resulted in the green map (lower right corner).  Interestingly, there seems to be a lot of highly regular radially smeared density, which I suspect to be some kind of artifact from the masking.To generate the mask, I used the following parameters in relion: lowpass filter map of 25 A, pixel size 1.08 A (from data collection parameters), 0.001 initial binarisation threshold, extended binary map 2 pixels, and an 8 pixel soft-edge.  I would greatly appreciate any advice on how to improve the post processing, or insight into whether something else might be going on to induce the potential artifacts.
>
> Thanks!
>
> Leo
>
>
>
>

-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
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Cambridge CB2 0QH, U.K.
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