[phenixbb] Question about scale of ED maps from phenix vs map coeffs when displayed in COOT

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Fri Mar 20 14:39:14 PDT 2009

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? 



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