If you want to display CNS maps in Coot and have them on the right
scale, then you need to do one of two things. Either:
1. Don't use the map file, use the reflection file containing the map
coefficients, or
2. Change the setting in CNS which controls the extent of the output
map. Instead of outputting a map covering a single molecule, you need to
output a map covering a whole asymmetric unit (or if you prefer a whole
unit cell).
The Xplor maps output by CNS are output in O mode, not Coot mode, by
default. This is due to a fundamental difference in understanding what a
map is between programs which work crystal space (e.g. Coot, Quanta,
XtalView) and those which don't.
Kevin
Pascal Egea wrote:
> Dear All,
>
> I am currently carrying the refinement of a structure and comparing the
> results obtained in Refmac, Phenix and CNS.
>
> While Phenix and Refmac write maps and their corresponding coefficients
> in mtz format allowing display of 2Fo-Fc and Fo-Fc maps in COOT, the
> corresponding Fo-Fc map as written by CNS does not show positive and
> negatives peaks. There is density but it does not look like why I would
> expect for a Fo-Fc map. Why is that?
>
> I am also surprised by the differences between maps and their contouring
> levels between Refmac/Phenix and CNS. Is the way to scale ED maps
> different between those programs? Can differences in the way to perform
> bulk solvent correction account for those differences?
>
> Thanks in advance for your suggestions.
>
>
> Pascal Egea
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