Section 4.4 Atom Colouring http://lmb.bioch.ox.ac.uk/coot/doc/coot/Atom-Colouring.htmli.e. add to your ~/.coot file | (set-colour-map-rotation-on-read-pdb-c-only-flag 1)|
Or use the preferences (only in newer pre-release versions): Edit->Preferences->Bonds->Bond Colours tick the box: Change colour for Carbons only B