Job: Validation (FSC)

FSC calculation.


This job runs FSC calculation using input half-maps. It can either use a provided mask, or generate a new mask by thresholding, dilating, and soft-padding of the input density. It can also optionally re-optimize the tightness of the FSC mask. It also outputs FSC plots in .txt and .xml format for EMDB compatibility. Read more here.

In CryoSPARC v3.3+, this job can now run GPU calculation and mask generation on the GPU for a substantial speedup.


  • a volume group containing two half-maps

  • an optional mask input containing a mask to use for FSC calculation


  • the final mask that was used (in case the mask was optimized or generated within the job)

Common Parameters

  • Generate new FSC mask instructs the job to create a new mask using the below parameters

  • Use Relative Threshold instructs the job to interpret the threshold provided as a fraction of the maximum density in the volume (so the value should be between zero and one). If this is turned off, the threshold is interpreted as an absolute value.

  • mask near (A) is the distance to dilate the mask in Angstroms

  • mask far (A) is the distance to softly pad the mask after dilation. The final mask contains ones until the near distance, and falls of to zero at the far distance.

  • Optimize FSC mask tells the job to run FSC mask auto-tightening to make sure the mask is as tight as possible without biasing the FSC curve

  • Override pixel size (A) tells the job to use a different pixel size than the pixel size recorded in the input half-maps. If there is a small error (a few percent) in the original pixel size used during processing, a new pixel size can be input here to override the old pixel size. This will scale the FSC plots correctly, and output the half-maps with the corrected pixel size.

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