Usually one doesn't want to look at negative contour levels of a map1, so Coot has by default a limit that stops the contour level going beyond (less than) 0. To remove the limit:
(set-stop-scroll-iso-map 0) for a 2Fo-Fc style map
(set-stop-scroll-diff-map 0) for a difference map
To set the limits to negative (e.g. -0.6) levels:
(set-stop-scroll-iso-map-level -0.6)
and similarly:
(set-stop-scroll-diff-map-level -0.6)
where the level is specified in e^-/\AA^3.
[1] in a coot difference map you will get to see the negative level contoured at the inverted level of the positive level, what I mean is that you don't want to see the “positive” level going less than 0.