JED's example is very illustrative and it shows that chirality may
need to be added to this link definition. then sugar validation may be
easier (at least ASN-NAG with only one sugar). If chirality is wrong
then rotate around ND2-C1bond as a rigid group. Just like you do with
rotamers. Here you have only two orientations.
Garib
On 21 Apr 2010, at 14:20, Paul Emsley wrote:
> Garib Murshudov wrote:
>> As I see there is no chirality definition for NAG-ASN link
>> (perhaps there should be but then people will be unhappy even more).
>> Only reason i can see for this flattening is conflict between
>> geometry and electron density. Your example shows that even if
>> electron density is weak it may play a role and correct
>> orientation of sugar may matter.
>>
>
> I agree, and with JED too. More tests suggest that if I put the NAG
> into the density the wrong way round, Coot will happily flatten the
> C1. So, my guess would be that if you rotated your NAG 180 degrees
> round a vector ~ NG--(midpoint of C3,C4) and re-refined, then things
> would improve.
>
> At the moment, there is no substitute for knowledge when building
> carbohydrates - it would be a substantial improvement I think if
> someone added intelligent carbohydrate validation tools into Coot.
>
> Paul.
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