[phenixbb] Real space refine of long side chains

Ashu Sharma ashuthesharma13 at gmail.com
Mon Nov 25 11:25:55 PST 2019

Hi Luca,

I had similar issue with refinement against a low resolution data. However,
choosing input model as reference model for restraints (with little bit of
playing around with weight factor) took care of this.


On Mon, Nov 25, 2019 at 2:12 PM Luca Pellegrini <lp212 at cam.ac.uk> wrote:

> 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...
> Best wishes,
> Luca
> Luca Pellegrini, PhD
> Department of Biochemistry
> University of Cambridge
> Cambridge CB2 1GA
> United Kingdom
> lp212 at cam.ac.uk
> tel.: 0044 1223 760469
> https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group
> @PellegriniLab
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