Hi all,
I want to creat a mask only covering a single helix for local refinement. And I generated the volume in ChimeraX like this:
However, when I imported this volume into cryoSPARC and had it dilated 2 pix, it became a sphere like this:
I have no idea what is wrong there. I used to creat masks covering lager region of interests and the masks generated were always normal. Is this because that my region of interest is too small?
Hi pywt901, I’m used to making large and small masks. This kind of problem only happens when I make a mistake with the threshold… not so difficult to forget to set it, or forget a 0 after the decimal point.
Yes, prob a threshold issue… but also I would not suggest local refinement on a single helix (unless it is an unusually long helix) - not enough signal.
Hi, Oli! I’m curious like, what if the single helix is the only place that I need to get a higher resolution? Should I include the peripheral region during mask creation?
the problem is, this approach will not work.
It doesn’t matter if you only want to get better res in a single helix - masking it alone and attempting local refinement will lead to severe overfitting and no improvement in density quality.
I would suggest local refinement of the entire domain/region, including this helix, or possibly 3D classification to separate out multiple conformations.
I see. Thx a lot! 
