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 <[log in to unmask]> wrote:
From: Garib Murshudov <[log in to unmask]>
Subject: Re: [ccp4bb] geometry problems with sugars
To: [log in to unmask]
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.
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