That looks to me as if the critical Chi definitions are inappropriate for Phe & Tyr!
On 9 Jan 2012, at 12:24, Robbie Joosten wrote:
> 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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