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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