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

Mayer, Mark (NIH/NICHD) [E] mayerm at mail.nih.gov
Fri Jul 10 19:51:45 PDT 2015

Hi Pavel,

Would reciprocal space refinement improve maps - or would all the improvement come from model bias? i.e. would maps look nicer, but with no new information content? 

I guess the difference from X-ray is that while each HKL has contributions from all atoms in the ASU, for an EM map converted to structure factors this is not true. Also, EM maps have substantial local resolution differences, and I don't understand how this would impact SF calculation.

I know that some in the EM community, who are not used to hands on (i.e. coot/O etc) real space refinement, are disappointed by the small radius of convergence for automatic real space refinement that is not guided by a human being sitting at a graphics terminal. I doubt that reciprocal space refinement would change that, but would Fo-Fc maps make it easier to choose between good and bad fits to EM maps?

I'm hoping that people with more experience will chime in; I believe this is an active issue for CCP4 (refmac) users as well.

From: Pavel Afonine [pafonine at lbl.gov]
Sent: Friday, July 10, 2015 9:56 PM
To: Terwilliger, Thomas Charles; Mayer, Mark (NIH/NICHD) [E]; PHENIX user mailing list
Subject: Re: Fwd: [phenixbb] [ccp4bb] Phenix; converting a map to structure factors

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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