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 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!

Best wishes,

Chris