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.
