Hi Mark,

Tom copied me your email.

As I'm sure you are aware there is tremendous interest in building into and refining against low resolution (by X-ray standards) EM maps. Could you comment to the phenix BB about whether its appropriate to convert maps to reciprocal space and use ML refinement?

While it is a possible way of doing this (and this is how it's been done in the past) I don't think it is a good route to follow. In case of cryo-EM your data is map, so why not just refine against the map? Why take a detour through reciprocal-space by converting map into structure factors (=manipulating your original data) and doing reciprocal space using refinement programs that were designed for crystallography?
With this in mind we have developed a new refinement tool in Phenix (it is still in active development!) called phenix.real_space_refine that is designed to refine atomic models directly into maps (any map: X-ray, neutron, cryo-EM, low or high resolution), for quick summary see

http://phenix-online.org/presentations/real_space_refine.pdf

as well as documentation page (at the bottom):

http://phenix-online.org/documentation/

and newsletter article (page 43):

http://phenix-online.org/newsletter/CCN_2013_07.pdf

Let me know if you have any questions or comments!

Pavel