Hi all, I’m having some trouble getting a high resolution structure from my 2Ds.
I’m hitting 6A and I cannot go further beyond that. My particle is small so I know that Cryosparc is using the micelle to center the particle.
The box size is 400 and I fourier crop to 200.
These are how some of the 2Ds look from my NuRefine at 6A with C3 symmetry. It’s quite noisy.
I think I need to center the 2Ds using the ECD but I’m not sure how.
Hi @nkoylas1
What is the CTF estimation for this micrograph? If the CTF looks good, you can extract these particles using a larger box size and then bin them down (for example, extract at 600 Å and bin to 200 Å). What is the pixel size for this dataset?
We have faced a similar issue in our lab with a 0.74 Å/pixel dataset. When we extracted with a larger box size, both the 2D classes and the refinement improved significantly.
Another possible issue could be the number of particles. Do you have more particle classes available, or are these the only classes you used for ab-initio and subsequent refinement?
Hi Nikhil, the bulk of the particles have CTFs less than 10. I picked CTF 20 and below.
The average CTF is 9.9
Pixel size before binning is 0.93 Å/pixel.
Box size 400; cropped to 200
