I’m comparing the numerical values of 3D maps and wonder, how are maps scaled at the output of your reconstructions? Do you normalize them to sigma for example? I’m curious because the CS maps I’ve seen have values ~1 while Relion’s maps have much smaller voxel values that seem to be related to particle image values.
Hi Fred,
CS uses an image formation model with a scale parameter (alpha). I don’t know the answer to your specific question, but test projections of a CS map need to be multiplied by alpha to be on the same scale as the corresponding particle. I also believe that the raw map from refinement is a sum of the two half-maps, and not an average (before FSC weighting).