EMDB FSC files in XML format

Utilities
1

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.

It’s not straightforward to re-run the job. I’ve tried running a script that had been posted on here previously to turn the .txt file into XML (GitHub - simonfromm/miscEM: Various tcsh and bash scripts for file handling and maniupulation of EM micrographs and data derived thereof. It is called [fsc_cryosparc2_to_emdb-xml.sh), but the resulting XML file was not accepted by the PDB.

Or does anyone have an example of the exact syntax of the XML file required by the EMDB?

Any help would be much appreciated.

2

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.

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3

Hi @becky,

An EMDB-friendly XML version of the best FSC is outputted by default in all jobs that generate FSCs. To generate XML versions of any Volume (and optionally Mask) output, use the Validation (FSC) job.
More details are in our guide, here: Guide: EMDB-friendly XML file for FSC plots - CryoSPARC Guide

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4

Hi @stephan - I think this was only added in v3.3 though?

5

The EMAN2 e2procxml command can also be used to convert between XML and TXT.

6

Hey @olibclarke, @becky,

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:

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