[phenixbb] Low resolution refinement

Pavel Afonine pafonine at lbl.gov
Tue Nov 6 00:47:33 PST 2018

Hi Ashu,

you can use phenix.dock_in_map to dock known pieces (from crystal 
structures) into cryo-EM map.

Then you can use phenix.real_space_refine to refine placed model into 
cryo-EM map. It is important that you use reference model restraints 
with high-res X-ray model as a reference.

What to do with side chains is a good question. I doubt you can see any 
side chains in 7A resolution map. Reference X-ray model is perhaps your 
best source of knowledge about the side chains. Though keeping them in 
the model in the absence of support from the data seems questionable. I 
doubt there is a clear cut consensus/answer to this.

You can vary the strength of reference model restraints do vary the dose 
of bias from the known (reference) model.


> Dear All,
> I am refining a ~7A single particle cryo-em structure of a protein. 
> The protein has two domains and high-resolution crystal structures of 
> individual domains are already known. I could fit these two crystal 
> structures in the low resolution cryoem map of the full-length 
> protein. I have two questions:
> 1) Is it acceptable to refine with side chains in this case? In most 
> of the cases, with the guidane from crystal structures, side chains 
> could be placed with reasonable confidence, particularly smaller ones. 
> Should I restrict to poly-ala model or take the advantage of crystal 
> structures and include side chains also?
> 2) When I tried to refine with side chains, longer side chains like K, 
> R, Q, E which have weaker density tend to bend towards the backbone 
> density. Is there a way to prevent this happening?
> Suggestions/comments from the community would be highly appreciated.
> Thanks !
> Ashu

More information about the phenixbb mailing list