[phenixbb] Question about restraints

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Fri Nov 12 13:16:15 PST 2010

Hi Ralf,

yes ligand has good geometry initially, i.e. after I generate it. During
placement in coot and refinement in phenix it gets a bit distorted. In
general I see these kind of problems in saturated, substituted ring
systems using medium resolution < 2.0 A. The density is not clear enough
to restrict the conformations of these ring systems, since it is
basically enclosed in a round blob of density. So the real space
refinement in coot and refinement in phenix take liberty from the
freedom given in the restraints (Sorry had to paraphrase DVD here...) to
fit the ligand in the ambiguous density. 
In this particular case, I am looking at a azepinene system (seven
membered ring containing one nitrogen and a double bond), which probably
has several low energy conformations close together, which muddles the
water even further.



> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of Ralf W. Grosse-Kunstleve
> Sent: Friday, November 12, 2010 3:46 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] Question about restraints
> Hi Carsten,
> > I am trying to tighten up the geometry of a badly behaving ligand
> Does the ligand have good geometry to start out with and is distorted
> during refinement?
> Ralf
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