[phenixbb] Real space refine of long side chains

Pavel Afonine pafonine at lbl.gov
Mon Nov 25 11:21:04 PST 2019

Hi Luca,
> I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards...

do you have an example that you can share (off list)? Ideally, the most 
helpful would be to have models before and after refinement, the map and 
chain/residue ids of problematic side chains.


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