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. Cheers, Carsten
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] 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?
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