Elaine & Tom -

Thanks so much for your help. The vop cover command worked perfectly, which is a bit embarrassing because I know you've posted on that before. 

I thought there was a rotation involved, which I guess reflects rather badly on my ability to compare electron density maps to models. 

I was also thinking that it was a more complicated transformation, because I could see that the Coot map headers include some symmetry operators that were different from the working Phenix maps. (symop=x,y,z versus symop= ). ChimeraX opens the map but returns this error:

Unable to parse symmetry operators of coot-map.ccp4 b'x, y, z

Either way, vop cover solves the problem.

gsb