On 30/09/2019 11:36, Chris Fage wrote:
>
> I recently obtained structures of a protein bound to two different small molecules. When viewing the
> structures in Coot with a similar contour setting, the 2Fo-Fc map around ligand 1 is clearly much weaker
> than that around ligand 2.However, after generating 2Fo-Fc maps in FFT
No need to do this - just export the map (or the map fragment).
> and loading them in Pymol (again,
> choosing equal contour levels), the maps surrounding ligands 1 and 2 have nearly the same quality. Is there
> a difference in scaling between the two programs that can account for this? Thanks for any advice!
How does the map from FFT look in Coot? I imagine that it would look just the same as the mtz map - but we
should rule out the generation of the map as a factor before proceeding.
As a side-note, when comparing contour levels between coot and PyMOL, be sure to use absolute levels, not rmsds.
Paul.
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