[phenixbb] Fwd: [ccp4bb] Phenix; converting a map to structure factors

Pavel Afonine pafonine at lbl.gov
Fri Jul 10 18:56:46 PDT 2015

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


as well as documentation page (at the bottom):


and newsletter article (page 43):


Let me know if you have any questions or comments!


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