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
