Maps can be re-contoured using the middle-mouse scroll-wheel (buttons 4 and 5 in X Window System(TM) terminology). Scrolling the mouse wheel will change the map contour level and the map it redrawn. If you have several maps displayed then the map that has its contour level changed can be set using HID -> Scrollwheel -> Attach scroll-wheel to which map?. If there is only one map displayed, then that is the map that has its contour level changed (no matter what the scroll-wheel is attached to in the menu). The level of the electron density is displayed in the top right hand corner of the OpenGL canvas.
Use keyboard <+> or <-> to change the contour level if you don't have a scroll-wheel 1.
If you are creating your map from an MTZ file, you can choose to click on the “is difference map” button on the Column Label selection widget (after a data set filename has been selected) then this map will be displayed in 2 colours corresponding to + and - the map contour level.
If you read in a map and it is a difference map then there is a checkbutton to tell Coot that.
If you want to tell Coot that a map is a difference map after it has been read, use:
(set-map-is-difference-map imol)
where imol is the molecule number.
By default the change of the contour level is determined from the sigma of the map. You can change this in the map properties dialog or by using the scripting function:
(set-contour-by-sigma-step-by-mol step on/off? imol)
where
step is the difference in sigma from one level to the next (typically 0.2)
on/off? is either 0 (sigma stepping off) or 1 (sigma stepping on)
By default the map radius 2 is 10Å. The default increment to the electron density depends on whether or not this is a difference map (0.05 e^-/\AA^3 for a “2Fo-Fc” style map and 0.005 e^-/\AA^3 for a difference map). You can change these using Edit -> Map Parameters or by using the “Properties” button of a particular map in the Display Control (Display Manager) window.