[phenixbb] Low resolution refinement

Ashu Sharma ashuthesharma13 at gmail.com
Mon Nov 5 23:43:51 PST 2018

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 !

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