Hi Phil, It is annoying problem especially for Phe and Tyr which have standard rotamers close to the critical chi angles (-90 and +90). Asp and Glu do not have standard rotamers near critical angles, so the problem should be much smaller (but I still get them too often). If Val, Leu and Arg problems reoccur after refinement, then there is something seriously wrong.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Phil Evans > Sent: Monday, January 09, 2012 12:54 > To: [email protected] > Subject: Re: [ccp4bb] chirality problem > > The problem with fixing the nomenclature "problems" in Coot is that they are > back again after the next round of refinement (or at least some of them are, > if they are right on the edge of an arbitrary distinction) - indeed irritating Phil > > On 9 Jan 2012, at 11:43, Paul Emsley wrote: > > > On 08/01/12 10:36, ccp4 wrote: > >> Won't coot fix the nomenclature issue, then you can check whether you > >> have a real chirality problem - eg a squashed flattened VAL.. > >> > > > > It will indeed [1]. So Afshan need only read in the file, Press OK and then > Save. > > > > Robbie and I think that it is more likely than not that Afshan did not really > have a chirality problem. > > > > Afshan and Kim have been in touch and confirm that it is the adit validation > report that describes a nomenclature error on a VAL CB as a chirality problem > (rather than anything from CCP4). > > > > Paul. > > > > > > [1] well, modern ones do [2] > > [2] and you can turn it off (some people find the feature annoying)
