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 could do this by exporting the coordinates and re-extracting in Relion, but that has been failing in the same ways as these posts (if I use passthrough files, i get the ‘Columns…’ error, if I don’t, it works, but RELION doesn’t know where the micrographs are (they have been MotionCorrected in Relion))
How to convert cs format to star format in cryosparc v2?
Exporting coordinates of picked particles
Exporting symmetry expanded particles
Maybe @DanielAsarnow could help with that?
What would make my life much easier would be to have the ability to re-center on an arbitrarily defined point in a 3D volume as I can do in Relion!