Hey again @rposert!
The main reason im using such a small part of the protein is because I thought I saw some densities in this region during 2D classification which then disappeared, so I wanted to investigate whether my binder might be ‘averaged out’ during the later refinement processes, and I didn’t know whether the variability analysis would work that way.
Thanks for the suggestions on improving the masks, the dust was something I also wondered about due to the tutorial - I’ve given both your suggestions a try now, subsequently, but sadly the error still appears (without adding a soft edge so far).
One thing I found a bit confusing is why the contouring is so drastically different for the one mask, showing all those spikey features as you also mentioned, while the other one does not.
Based on the answer you’ve given on the forum previously (Question about how masks are used - #2 by rposert), I understand that’s not something that can be changed by adjusting the thresholds in ChimeraX, but is actually done by applying the soft edge correctly, right?
So I guess the last thing to try is to get that right somehow. Is there any faster way to check the resulting masks other than downloading all attempts and opening them in Chimera again?
In any case, thanks a lot for taking a look at this!