Couldn't see secondary structure in a 2.9 Armstrong Map

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?


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)

Hi Olibclarke,

The distribution map looks like this:

Do you think it has a preferred orientation?

Yes, I would say it likely does

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