You can't read an Xplor map from phenix into coot and get the right
contour levels UNLESS you change your phenix settings to output a map
covering the unit cell instead of the molecule.
The Xplor maps output by phenix are output in O mode, not Coot mode, by
default. This is due to a fundamental difference in understanding what a
map is between Coot and older programs.
A better solution is not to use the maps at all, and use the mtz output
by phenix for this purpose.
Schubert, Carsten [PRDUS] wrote:
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
