Hello, everyone! I am a rookie to Cryo-EM data processing. I encountered a problem that I got a good class of particles after Ab-Initio Reconstruction but the density became worse after NU refinement. The parameters for NU refinement were default except that the Initial lowpass resolution (A) was changed to 10 Å. Any ideas about that?
the map colored by yellow is the initial model and the gray one is the map after NU refinement.
This looks like a very small molecule. In such cases, the dynamic masking procedure in NU-refine often makes things worse - I would suggest switching it off (by setting the start resolution for dynamic masking to 1Å).
Alternatively, you can try initiating local refinement starting from the poses you have generated with ab initio.
Hi @olibclarke ,
Thank you for your suggestions. I have tried to set the start resolution for dynamic masking to 1Å during NU-refinement but got similar result as before. I also tried local refinement using the initial model and corresponding particles without any improvement on map density. I wonder whether the strong micelle signal will hamper the resolution and how to solve this problem?
I have met the same question with Verdandy AND I just tried your method which is initiating local refinement starting from the poses you have generated with ab initio.. However, it always failed and showed I should put some half sizes. I try two kinds of local refinement, but both failed. So, is anything wrong with my operation ? Thank you.