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.
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
initial resolution 10-20
final resolution: 5-10
What are you suggestions for the hom. refinement job?