Hi Grzegorz,
Chimera doesn’t support making the transformation from 3d grid indices to physical coordinates containing an inversion. In theory it could since it just treats this transformation as a general affine transform (multiplying by an arbitrary 3x3 matrix, then shifting by a 3-vector). But to make it easy for users to control this transform it converts it into a rotation axis and angle, scale factors, and skewing, and does not include the possibility of inversion. So if you read a Chimera *.cmap file or some otther format (e.g. DX used by APBS maps), you will get an error from Chimera. In principle the file formats that allow a 3x3 matrix can handle it, but Chimera cannot. On the rare occassions when Chimera users have wanted to change the handedness of a 3d image the standard approach is to flip the z-stack of images with command "vop zflip #2” as Elaine mentioned.
There are more problems with left-handed coordinate systems for maps in Chimera. Contour surface normal vectors will point inward instead of outward messing up the lighting appearance.
Tom