Stuck email... try again... -------- Original Message -------- Subject: Re: [ccp4bb] sugar and coot Date: Wed, 30 Nov 2011 19:42:54 +0000 From: Paul Emsley <paul.ems...@bioch.ox.ac.uk> To: d...@iwonka.med.virginia.edu <d...@iwonka.med.virginia.edu> CC: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
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.
