FSC curve does not include Nyquist

Features and Functionality
1

Dear Cryosparc Community,

Is there a way force the FSC curve to include Nyquist. For example, one of my datasets clearly do not extend beyond 3.4 Angs as the FSC values reaches 0 around 3.6 and naturally Cryosparc shows the values up to 3.4. However a reviewer have asked that I did extend the range to include Nyquist, which for this dataset is 2.8.

Any suggestions on how to get those values or calculate the FSC curve fully to include Nyquist?

Best,
Omid

2

Hi Omid,

You can easily calculate a FSC using relion_postprocess, using the same mask and half maps generated by cryosparc.

Cheers
Oli

3

Hi Oli,

Thanks for the tip. I don’t know why I didn’t think of that. Also in case anyone else is trying this. You need to change the file name to match what Relion requested, so half1_unfil.mrc otherwise you get an error.

Cheers,
Omid

4

Hi Omid - you only need to change the name if you only provide one half map. If you provide both as --i and --i2 I believe you can call them whatever you like, although I could be mistaken

Oli

5

Hi Oli,

Yup that works. Sadly the curve still stops short of Nyquist even in relion.

Best,
Omid

6

That doesn’t seem right. Are you sure you didn’t run the refinement in a smaller box size than the actual box size of the particle images?

1 Like
7

Hi Oli,

Yes the refinement was downsized for some reason. I am working one someone else is dataset trying to backtrack what they did. Just checked the refinement settings and indeed the particles were downsized compared to the original box six of the particles. It all makes sense now. Thanks for the help!

1 Like