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.
