(1) what is the scale units for the Real space slice heat map?
(2) is the Viewing Direction Distribution map 0,0 relative to the first view in the Real space slice?
a. Also is there a way to get a 3D angular distribution plot just to view it in 3D? I do like the heatmap output - just wanted to get a another perspective if possible.
The scale of real-space slices is the arbitrary units of density from the particle images themselves, so it’s related to electron density, but depends on ice thickness, beam brightness, sensor MTF, any preprocessing, etc.
The azimuth=0 elevation=0 point on the heatmap should correspond to the first of the real-space slices.
Unfortunately right now we don’t have a direct output of a 3D angular distribution plot. I’m not sure if it’s possible but you can convert the .csv output of a refinement job to a .star file, then use that in Relion to create the 3D angular distribution plot.