I have a conformationally heterogenous protein that I am slowly having success with. One thing that has been working is to pick and extract using the LoG picker in Relion, performing most of the classification in CryoSPARC, and then re-extracting the particles after re-centering based on where I know the rest of the protein is. I have also found some success using 2D templates from that to do template-based picking in CryoSPARC, but now I’d like to re-center and re-extract in a small box size just on the part of the protein that has been hard to resolve.
I strongly agree that this would be a phenomenally useful feature!
We often work with systems where the ability to re-extract (even multiple) subparticles would be very
useful. An ideal implementation would be the ability to simply point-and-click on one or multiple spots
within a 2d calss average, then specify box size and re-extract these subparticles into new particle stacks.
In cryoSPARC 3.0+, once you’ve done the local refinement as sugguested by @Lucas you can then re-extract and re-center the particles using the new origins.
are there plans to include shifting during re-extraction in CS any time soon? I feel like this is a really useful feature and running local refinements is a lot of work if the same could be achieved with a simple shift during re-extraction.
This will be coming in the next release — we will be adding a utility to shift volumes + particles so that re-extraction can be done with particles shifted to any desired origin in 3D space.