Hi, we’ve run Cryosparc v3.2 for a project that we’ve just submitted to the PDB. We’ve now got v4.0.2 installed. What is the best way to obtain our FSC curve for deposition to the PDB? It needs to be in EMDB-friendly XML format.
You can also just recalculate the FSC using relion_postprocess - using the cryosparc half maps & FSC mask. You may also want to inspect the fsc_auto mask generated by cryosparc to make sure that it is sensible - quite often at least for membrane proteins it is not, and in this case you may want to make your own mask for the final FSC calculation.
If you’re running v3.3+, and you have a v3.2 job that has volume or (optionally) mask outputs (e.g., a Homogeneous Refinement job), you can connect those outputs to a Validation (FSC) job. This job will generate new FSC masks or, given a Mask input, recreate FSC plots. This job will always write corresponding EMPDB-friendly XML files to the job directory.
If you don’t have the v3.2 job anymore, you can always import the half maps using Import 3D Volumes, and connect those outputs to a Validation (FSC) job.
If you are running a version of CryoSPARC earlier than v3.3 (the version that outputting EMDB-friendly XML versions of FSCs were introduced), you will have to use one of the methods described by the users here, or use this script: