Hello, I have a 120A protein. And the data was collected on 0.8A pixel detector. I extracted the particles with a box size of 360 pix following direction on How big should my particle box be? – The Jiang Lab.
With 500,000 the resolution is only 6A at best while I was expecting to be <4A. I read that the smaller size gives better resolution as discussed here: Why does smaller box size give better resolution?.
Now I want to refine with a smaller box size. Is there a way, I can just reduce the particle box size of the already extracted particles? Rather than re-extracting the particles with smaller box size?
With 360 pix, there were already over 10million particles to pick and I fear with a smaller box, the number will increase further.
you can ‘window’ in real space in the refinement job. or the utility you are looking for is ‘downsample particles’ but effectively it is the same as re-running extraction (it takes a long time and duplicates the data). Might I suggest you start with classification in 2D and 3D to quickly remove as many particles as possible which obviously won’t contribute to your best reconstruction, then you will have to change the box size of only <1 million particles let’s say.
I found out the “Extract micrograph” job takes particle stack as an input as well. So if you give the micrograph and the particle stack (with large box) as input, and change the parameter to smaller box size, it will extract only those particles with small box size saving space and time. Great!