[phenixbb] secondary structure restraints helices/helixes proline

Nathaniel Echols nechols at lbl.gov
Thu May 3 17:17:09 PDT 2012

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)?


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