Re-centering particles based on an arbitrary center during extraction

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.

  1. 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?

  2. 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!



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.


Dear all,

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.


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Hi @ClaudiaKielkopf,

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.



Thanks Michael, that’s great to know!

Michael, do you have an estimate as to when the release containing this utility will be available?


The Volume Alignment Tools utility, introduced in v3.3.1 (released December 1, 2021) supports this functionality. Please see for more details.

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