Hi,
> However, at this stage, I had warnings that my angular accuracy was worse than 10 degrees in 3D refine.
Having this warning during the first few iterations is harmless.
Didn't it resolve spontaneously after later iterations?
> I re-ran 3D refine and also enabled local search in 3D refine by giving the same value (1.8) for 'Initial angular sampling' and 'local searches from auto-sampling'.
What happens if you don't do local search?
> But the resolution is much worse than what I get with the 3D classification routine. I look at the output map and it looks as my molecule should but low pass filtered. I am trying to figure out why 3D auto refine procedure gives a map that is almost 5-6 angstroms worse than the 3D classification output map.
Class3D does not perform gold-standard separation, so it tends to
overestimate resolution. Nonetheless, the difference of 5-6 A is
too big. Something is wrong.
We need more information:
- Did you use a mask during Class3D and Refine3D?
- Did you use 'solvent flattened FSC' in Refine3D?
- Where did your initial model for Class3D and Refine3D come from?
- How much low pass filtering did you apply to it?
Best regards,
Takanori Nakane
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