Small particles processing

3D Refinement
1

Dear all,
I have a small protein (100kDa). I am aware of some settings that will improve 2D and ab-initio when it comes to smaller proteins/particles.

2D:
Force max over poses/shifts: OFF
Number of final full iterations: Increase to 10-20
Number of online-EM iterations: increase to 30-80
Batchsize per class: Increase to 200-300

ab-inito:
initial resolution 10-20
final resolution: 5-10
batchsize: increase

What are you suggestions for the hom. refinement job?

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2

For small proteins, try Non-uniform refinement. It works better than homogeneous refinement for small proteins in my experience. I’ve found if the sample is concentrated, adjusting the inner windowing radius so it’s fairly close to your particle can help (but be careful not to make it too close…!)

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