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:[log in to unmask]] On Behalf Of
> Phil Evans
> Sent: Monday, January 09, 2012 12:54
> To: [log in to unmask]
> 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)
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