3d homogeneous refinement - proper masking

3D Refinement
1

Dear colleagues,

Could you please prompt how to deal with result variation during 3D homogenious refinement -
Sometimes during the refinement, the background becomes green or even yellow.
Is this an issue of dynamic masking or noise estimation?
What is the proper way dealing with such cases?

Example -

Usual background
image

Problem background
image

Can I use the vertical scale in the Real Space Slices Iteration window to adjust the mask/noise level?
Please advise.

Thank you.

Kind regards,
Dmitry

2

I think it’s to do with normalisation - CryoSPARC is a lot less fussy (more forgiving) about normalisation than, e.g. RELION. I see background colour variation throughout a run, as more particles get added to the refinements.

1 Like
3

Thank you @rbs_sci. I thought there is a way to adjust some parameters of the dynamic masking based on the scale to fix that.

Kind regards,
Dmitry