Re-centering particles on different coordinates

Particle Picking
1

Hi!

I’ve had great luck using cryoSPARC from pre-processing to performing 3D homogenous refinement on my single particle data.

However, I am working with a protein complex whose N-terminus is much less stable than its C-terminus. Therefore, cryoSPARC likes to pick particles and align primarily based on the C-terminus.

I would like to perform “split” processing, i.e. take the particles that are aligned on the C-terminus then re-center the particles using an offset in the y-direction, then refine based on the new coordinates to resolve the N-terminal region.

We are used to doing this in RELION for several other samples from our lab, but I’m not entirely sure if it’s possible to do this with a particle stack from cryoSPARC or how I would go about doing so.

Any input is gladly appreciated!

Best,

Mia Shin
Graduate Student
Scripps Research
Lander and Wiseman Labs

2

Hi Mia,
You can use particles extracted from Relion with your alternate center, and import them into cryosparc. Or, you could convert from .cs to .star using csparc2star.py, recenter them using subparticles.py --target=x,y,z (both are part of pyem), and then import those without re-extracting. Final option, entirely in cryosparc but limited to local alignment searches, is to use the local refinement job and set the fulcrum point to your x,y,z target for those particles.

PS Cristina says hi :slight_smile:

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