Hi there, I have a question regarding box cropping after particle subtraction in CryoSPARC. I performed particle subtraction using a large box size (560 px), followed by a homogeneous refinement as a sanity check. It now seems necessary to crop the particles and volume down to 360 px to achieve better resolution and for further downstream processing.
I’m unsure how to do this properly. I came across a thread suggesting that the Volume Alignment Tools job could help, but I’m not confident about the required parameters for re-centering, such as the 3D coordinates and rotation settings.
If I go this route, would I also need to re-extract the particles with the new desired box size (360 px)? And if so, would this re-extraction apply only to the subtracted particles or to the original particles as a whole?
Any advice or clarification would be appreciated—thank you!