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...? Pavel. 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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