Hi Smith,

if you've got cryo-EM map, built an initial model into it and want to refine it then the most natural way to do so is to refine the model against the map directly and NOT take a detour through reciprocal space by converting the map into structure factors and then using the crystallography-specific refinement programs.

There is a Phenix refinement tool specifically designed for this - refinement of atomic models into cryo-EM maps or low-resolution X-ray maps, described here:

https://www.dropbox.com/s/imv2yzwodik13in/afonine_etal_wcpcw2015.pdf?dl=0

If for whatever reason you still want to do it the old way, then here are two steps:
- convert the map into structure factors:
phenix.map_to_structure_factors map.ccp4

- then run phenix.refine the usual way.

More info at the bottom of this page:

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

Pavel

On 4/4/15 6:38 AM, Smith Liu wrote:

Dear All,

Recently there are cryo-electronic microscopy papers which refine the reciprocal space of the electronic mcroscopy map by phenix refine. For the electronic mcroscopy map, what does it mean for the reciprocal space? How to get the reciprocal space map from the electronic mcroscopy map? In order to realize this kind of refine in phenx, we only process the xyz coordinates strategy refine in the graphical interface, right?

I am looking forward to getting your reply.

Smith
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