[phenixbb] secondary structure restraints helices/helixes proline

Morten Groftehauge mortengroftehauge.work at gmail.com
Fri May 4 08:01:10 PDT 2012

I'm sorry, phenix.refine seems to be treating the prolines entirely


On 4 May 2012 01:17, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Wed, May 2, 2012 at 9:20 AM, Morten Groftehauge
> <mortengroftehauge.work at gmail.com> wrote:
> > How does phenix.refine handle prolines in helices? When I look in high
> > resolution structures it seems that the carbonyl of the residue four
> > positions before the proline (also in the helix) should be more
> > perpendicular than parallel to the helix. This makes sense since there
> isn't
> > any nitrogen for it to hydrogen bond to.
> > But when I refine my structure it seems as if phenix.refine is trying to
> > push the carbonyl into parallel position. Am I imagining things? It's not
> > the best data and this is a troublesome region.
> Are you using the secondary structure restraints?  If so, it is likely
> a bug - could you please send me the input model (no data necessary
> for this)?
> thanks,
> Nat
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Morten K Grøftehauge, PhD
Pohl Group
Durham University
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