Thanks Kevin,

I'll give calculating the maps over the whole unit cell a try. Although if I understand Ralf correctly the summation is done over the whole Unit Cell. Usually I use the map-coefficients, since they are more convenient anyway, but for presentation graphics programs like PyMol and for specialized maps, like the new "kicked" maps, map-coeffs are not (yet) an option. 

Cheers

	Carsten

-----Original Message-----
From: Mailing list for users of COOT Crystallographic Software
[mailto:[log in to unmask]]On Behalf Of Kevin Cowtan
Sent: Sunday, March 22, 2009 4:27 AM
To: [log in to unmask]
Subject: Re: [COOT] Question about scale of ED maps from phenix vs map
coeffs when displayed in COOT


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
> 
> 
>