Window Dataset -- When to use?

Cryo-EM Data Processing
1

Hi all,

I am wondering when to use “Window dataset” for 2D and 3D. I understand the principle: circular masking the cropped particles to improve cross correlation. For 2D this is distinct from ‘circular mask’ which applies a mask to the 2D class averages.

However, I have tried altering the “Window Dataset” but it doesn’t improve the map at all, even when the particles came from highly packed micrographs. It’s a bit confusing, since I would expect that correctly using this parameter should improve alignment since it occludes neighboring particles, but it seems to make no difference. Is there an explanation for this, and can someone explain when they think that modifying this parameter might actually have a noticeable impact?

Thanks!

2

You don’t want to use window dataset (which windows the particles), you want to change the circular mask radius (which is applied to the classes) - try that? Definitely helps with crowded particles!