Couldn't see secondary structure in a 2.9 Armstrong Map

3D Refinement
1

Dear all,

Recently we processed one CryoEM structure to 2.9 Armstrong from Cryosparc, the FSC curve looks ok. However, when we took a look in Chimera and Coot, the structure doesn’t really looks like that, we couldn’t identify a clear secondary structure; furthermore, if we were trying to fit the an alphafold prediction pdb into the map, we couldn’t fit in.

I wonder do you know how could this happen? Is there any ways we can do to improve the map?

Thanks!
P11_J87_fsc_iteration_006_after_fsc_mask_auto_tightening

P11_J87_fsc_iteration_006_after_fsc_mask_auto_tightening_chimera
P11_J87_fsc_iteration_006_after_fsc_mask_auto_tightening_chimera1920×968 66.1 KB

2

Hi @Ruoxi, what does the orientation distribution look like? If I had to guess I would say you have preferred orientation (only one or a limited number of views)

3

Hi Olibclarke,

The distribution map looks like this:
P11_J87_viewing_direction_distribution_iteration_006
P11_J87_posterior_precision_directional_distribution_iteration_006

Do you think it has a preferred orientation?
Thanks,

4

Yes, I would say it likely does

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