Dear all,

I'm trying to do the subtomo averaging by Relion3.0. I read the article published on nature protocols, it says the box size of 3dctf should be set to the same values as that used in the ‘Particle box size’ command. But what if I want to trim or bin the subtomo I extracted?

For example, I use bin1 tomogram and the corresponding box size is 300. When I extract the particle I write 300 in "Particle box size" and 200 in "Re-scaled size", which means I want to calculate binned particles first, then is that ok if my 3dctf size is 300? And what if I want to re-extract particles from bin1 tomogram with different size, for example  200 "Particle box size" and don't rescale particles, should I calculate 3dctf again with size 200? I think binning and trimming of subtomo corresponding to different operations of pre-calculated 3dctf, can relion distinguish it automatically?

By the way, I find the calculation of 3dctf is very slow when the size is big. The paper says 3dctf is calculated by tri-linear interpolation on Cartesian grid and then multiply by a weight matrix, and I think the calculation of weight matrixes cost most of the time. Are weight matrixes of different particles from one tomogram the same, considering they have the same 2dctf slices position? Can it just calculate weight matirx once for each tomogram other than each particle? I don't know how to output the weight matrix.

Thanks,
X Yan

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