On Thu, 22 Apr 2010 10:13:40 -0700, tirumal wrote:
> 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 th
I am trying to resist answering ccp4bb ... but
> Thanks to all who responded. 180 degrees flip of the problematic NAGs,
> did help. 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
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 wrote:
From: Garib Murshudov
Subject: Re: [ccp4bb] geometry problems with sugars
To: CCP4BB@JISCMAIL.AC.UK
Date: Wednesday, 21 April
tely 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 wrote:
From: Garib Murshudov
Subject: Re: [ccp4bb] geometry problems with sugars
To: CCP4BB@JISCMAIL.AC.UK
Date: Wednesday, 21 April, 2010, 9:58
JE
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
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
cmail.ac.uk] On Behalf
Of Paul Emsley
Sent: 20 April 2010 23:57
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] geometry problems with sugars
tirumal wrote:
Hi All,
My question is concerning geometry of NAGs in a glycoprotein
structure.
Fire away...
I recently solved the structure of a gl
ssage-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul
Emsley
Sent: 20 April 2010 23:57
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] geometry problems with sugars
tirumal wrote:
> Hi All,
>
> My question is concerning geometry of NAGs in a glycoprotein
tirumal wrote:
Hi All,
My question is concerning geometry of NAGs in a glycoprotein structure.
Fire away...
I recently solved the structure of a glycoprotein to 3 Å and modeled
NAGs linked to Asn at 3 different places. NAGs and Asn-NAG links are
refined in Phenix.refine as per the Pheni
Hi All,
My question is concerning geometry of NAGs in a glycoprotein structure.
I recently solved the structure of a glycoprotein to 3 Å and modeled NAGs
linked to Asn at 3 different places. NAGs and Asn-NAG links are refined in
Phenix.refine as per the Phenix dictionary.
However, when subm
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