Hi,
Sorry for the crosspost, but I am not sure were the problem is located:
I noticed that the xplor maps generated by phenix seem to be on a different
scale than the maps generated from the map-coefficients from the same
refinement run when the maps-coeffs are read into coot. Usually I only read in
the map-coeffs and the scale seems reasonable to me, i.e. average density ~0.28
e/A3 at 1 sigma for a 2fofc map. The map from the same run (converted to ccp4
map in mapman) is at 0.55e/A3 at 1 sigma, when displayed in coot.
The map should be normalized in phenix (apply_sigma_scaling=True) and the stats
from mapman indicate an RMS deviation of ~1. For fofc maps I need to crank up
the display to 6 sigma to get an equivalently looking map as the one from the
map-coefficients at 3 sigma contour level. Any hints as to were the factor of 2
comes from, coot or phenix?
Cheers,
Carsten
