Hello, I was trying to test if the microtubule seam-alignment procedure can be done directly via cryosparc and I am referring the MiRP v2 protocol shown below:
I was wondering, if there is equivalent parameter setting in local refinement job I could use to approximate this RELION-based refinement setting? Thanks a lot.
Hi @nym2834610!
You’re following this protocol, right? Could you give me a bit more information on what exactly this protocol does, and which parameter you’re hoping to find a match for here?
Thank you!
Thanks for the replying.
Yes. I basically want to test if the small angle local refinement process in RELION could be done via the local refinement job in cryosparc. In other words, for example, if I want to perform the local-search by specifying tilt at 15, psi 10 at RELION, what should I do in the local refinement job? Currently what I did was as shown:
I see! Thanks for explaining what you’re looking for!
Unfortunately, right now, you cannot control the search space of each angle individually in CryoSPARC. Therefore, setting the overall angular search extent to 15° as you have is probably what I’d try, but I do not know enough about this process to know whether that will be sufficiently similar to what is done in RELION.
Sorry I can’t be more help!
The last setting you need for Relion-like search behavior are “re-center poses/shifts each iteration.”
You can’t use different search ranges for each DoF, but this is mainly useful in Relion because the Euler angles have different domains. This doesn’t apply to the axis-angle representation used by cryoSPARC.
Thanks a lot for replying. I notice when turning on the recentering poses, sometimes it crashed in the last iteration with ‘No better angle is found’ error leading to NaN in FSC curve.
