[phenixbb] Heme geometry restraint

Gerard Bricogne gb10 at globalphasing.com
Tue Jul 21 11:26:47 PDT 2020

Dear Paul,

     Nice story: constrain and watch whether the data complain - otherwise
"Where freedom is given, liberties will be taken".

     And did you see significant difference density after enforcing

     With best wishes,


On Tue, Jul 21, 2020 at 07:13:49PM +0100, Paul Emsley wrote:
> On 20/07/2020 01:20, Yangqi Gu wrote:
> > Dear all,
> > I have a question regarding the heme c geometry restraint. I am aware
> > that heme c could undergo distortion when bound to protein, but I am not
> > sure at what resolution I could claim such distortion (such as
> > ruffling/bending/doming). I have a map at 3.6 A resolution and whenever
> > I did the refinement in phenix with real space refinement, some of the
> > hemes are distorted and I am wondering if it is justified to leave it
> > that way or do I have to impose the flat plane geometry. If so, how
> > should I proceed to impose such geometry? Thank you in advance!
> > 
> During my PhD I was fortunate enough to sit down at the graphics (a E&S
> PS390) with Michael Rossmann to show him my current Hb model. He expressed
> some scepticism about the way I had modelled the heme. "Make it flat and
> show me the difference map" he said. The point being that if it truly was 
> buckled then we'd see several significant difference map peaks (at say 3.0
> rmsd) around the pyrroles (not the Iron atom) consistent with the buckled
> model.
> Paul.
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