How to go from Cryosparc refinement to Relion Post processing?

3D Reconstruction
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Hi everyone,

I was wondering what is the best way to approach taking a map from non uniform refinement in cryosparc to relion post processing? The post processing requires a half map file could I just use the half map generated from cryosparc? What is the best way to go about this?

Thanks

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I would convert your cryoSPARC refinement to a star file using csparc2star.py then run Refine3D using local searches (set “initial sampling” and “local searches from” to the same value). You can force convergence, or create a mask and find the right parameters to get a good result from Relion local search. Typically, the angles from cryoSPARC are very good and convergence will be rapid and at approximately the same resolution. Afterwards, you can proceed through Relion as normal.

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Thanks for the reply and information. Just wondering, how would you go about forcing convergence?

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Can’t you also just put the A & B half maps into ‘relion_postprocess’ along with the fsc_auto mask? Or am I missing something (most likely the case)?

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The A & B halfmaps from cryoSPARC are just raw reconstructions with no filtering or masking applied, so they should be usable (with masks from cryoSPARC or elsewhere) in any post-processing tools

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@adtaheri There is an argument for forcing convering in Relion (I can’t remember exactly, should be in the expert section if you run relion_refine with no arguments). Usually this is used to run a final iteration on CPUs when the GPU doesn’t have enough memory for the converging iteration.

@apunjani and @olibclarke are correct that you should also be able to use the half-maps directly via the command line. The GUI and some command-line options in Relion do only accept a seed name that’s used to automatically find files with different endings, and some other operations like polishing etc. now require optimiser files, so sometimes it’s useful to create something that looks like a Relion job structure.

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for relion_postprocess, you can use the --i and --i2 flags to input both half maps manually

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