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.

Pavel

> 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