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

Pavel Afonine PAfonine at lbl.gov
Fri Mar 20 16:12:54 PDT 2009

That was (and is) always a mystery for me: when I look at two maps (both 
coming from phenix.refine):
- one is computed in COOT from phenix.refine map coefficients, and
- another one displayed in PyMol using X-plor formatted map.

To make both maps looking identical I have to draw them at different 
sigma levels, sometime very different. This is true for both fo-fc and 
2fo-fc maps.

I have some ideas but no any proofs so I don't want to put my 
speculations to the bb. So, I have no answer... May be Ralf or Paul E...?


On 3/20/09 2:39 PM, 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
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