Stuck email... try again...
-------- Original Message --------
Subject: Re: [ccp4bb] sugar and coot
Date: Wed, 30 Nov 2011 19:42:54 +0000
From: Paul Emsley <[log in to unmask]>
To: [log in to unmask] <[log in to unmask]>
CC: [log in to unmask] <[log in to unmask]>
On 30/11/11 17:07, Heping Zheng wrote:
>
> The issue I have is to polysacchride chains refinement in general, but
> here more specific about branch chain of polysacchride chains. For
> example, if you think about the case of N-glycosylation
> Asn-NAG-beta1,4-NAG-beta1,4-Man-(alpha1,3-Man)-alpha1,6-Man ...
>
> Now you have a branch chain, Now if I assume the following resseq
> ASN A135
> NAG A500
> NAG A501
> MAN A502
> MAN A503
> MAN A504
>
> In my coot, version 0.6 revision 2540, You will be able to refine
> A500-A503 as a whole since they are consecutive in resseq.
indeed.
> But when I need
> to refine NAG A500 together with ASN A135 locally, simply specify the
> range is not enough, I need to specify a small radius to get it work, even
> though the covalent link is defined in LINKR record.
Quite so. As I said (or more accurately, implied) LINKR recognition is
an on-going issue (i.e. it doesn't work yet).
> The same applies when
> I want to refine just A502-A504 alpha1,6 glycosidic bond without refine
> A503.
Yes.
> I am just wondering what is the state of the art for branch chain handling
> in coot or another interactive refinement program.
Well, I don't know much about about other programs, but in coot you can
use refine-residues or Sphere Refinement.
Even in 0.6.
Paul.
|