Pixel Size After 2D Class

2D Classification
1

I am observing that the pixel size of my 2D class averages/templates does not match the extraction pixel size. For context, I extracted particles with box size 280 without any Fourier Cropping. The pixel size is 1.1. Thus I would expect the whole image to be 308 A. But when I look at the MRCs in Fiji and set the scale as 1px=1.1 A, it appears the image is much smaller. Obviously, I did not downscale.

image

It appears cryosparc is doing some binning. When I download the template/2D Class average PNGs, the PNG dimensions are 128x128 (not the 280x280 I specified in extraction). This leads to a few questions:

  1. Is it fair to assume the pixel size scales as the box size (i.e. new pixel size is 1.1 * (280/128))?
  2. Is cryosparc downscaling? If not, how can we get PNG output with the same dimensions as the extraction?
  3. Is cryosparc downscaling? If so, how can a user prevent that?
2

Hi Jacob

Cryosparc will downsample on the fly during 2D according to the maximum resolution set in the 2D class parameters.

To be clear, this only applies to the 2D classes themselves - the output particles are unaltered. If you want 2D classes that are larger, you can change the maximum resolution, while keeping the maxium alignment resolution the same.

Cheers
Oli

3

Interesting. Helpful to know that the “maximum resolution” paramter effects only the pixel size of the templates/2D classes. Thanks Oli. Ill toggle the maximum resolution to get the correct pixel size in the 2D classes/templates.

BTW, love your YouTube video on Coot/Chimera. I use the plugins/coot-preferences daily.

~Jacob

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