I am trying to refine an icosahedral virus structure. Refinement works fine when using bin8 and bin4 data, but it continues to fail with bin2 data. The box size for bin2 data is 760 pixels. It appears that this is the limit currently. I do have information beyond bin4, so I have to refine it using bin2. Is there any way to overcome this issue?
Thanks a lot.
This won’t work in CryoSPARC if you are using an <=11GB card, and unfortunately there is no way to get around this limit that I am aware of.
Relion has the option to skip Fourier padding during reconstruction, which allows one to accommodate larger box sizes at the expense of some minor artefacts near the corner of the box - cryoSPARC unfortunately does not have this option.
I would suggest either moving to Relion, or re-extracting in a smaller (tighter) box).