The “graphics” window is drawn using OpenGL. It is considerably smoother (i.e. more frames/sec) when using a 3D accelerated X server.
The view is orthographic (i.e. the back is the same size as the front). The default clipping is about right for viewing coordinate data, but is often a little too “thick” for viewing electron density. It is easily changed (see Section Clipping Manipulation).
Depth-cueing is linear and fixed on.
The graphics window can be resized, but it has a minimum size of 400x400 pixels.
Hardware Stereo is an option for Coot (Draw -> Stereo... -> Hardware Stereo -> OK), side-by-side stereo is not an option.
The angle between the stereo pairs (the stereo separation) can be changed to suit your personal tastes using:
(set-hardware-stereo-angle-factor angle-factor)
where angle-factor would typically be between 1.0 and 2.0
When asked to pick a residue or atom, the cursor changes from the normal arrow shape to a "pick" cursor. Sometimes it is difficult to see the default pick cursor, so you can change it using the function
(set-pick-cursor-index i)
where i is an integer less than 256. The cursors can be viewed using an external X program:
xfd -fn cursor
A yellow box called the “origin marker” marks the origin. It can be removed using:
(set-show-origin-marker 0)
Its state can be queried like this:
(show-origin-marker-state)
which returns an number (0 if it is not displayed, 1 if it is).