Thanks to all who responded. 180 degrees flip of the problematic NAGs, did help.
> 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. If you have a poor density (which I guess, generally is the case for large glycoprotein structures) you have to depend on trial and error strategy to get the right NAG conformation. I don't know how other refinement programs handle this, but after Phenix.refinement run, one has to definitely check the geometry of the NAGs carefully. Hope to see a validation tool for NAGs in Coot soon. Tirumal --- On Wed, 21/4/10, Garib Murshudov <[email protected]> wrote: From: Garib Murshudov <[email protected]> Subject: Re: [ccp4bb] geometry problems with sugars To: [email protected] Date: Wednesday, 21 April, 2010, 9:58 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.
