Hi Jiamu,
You can use Sketcher to make the library for Coot.
You'd better to get the PDB file from
http://www.dkfz.de/spec/glycosciences.de/tools/pdbcare/ .
Good luck!
liu
Jiamu Du wrote:
Thanks for all the replies above. I have pasted the figure of the
electrondensity map in the attachment. It seems I can fit two NAC
molecules into the density. Any more suggestions are appreciated.
The remaining questions is below:
How to refine the NAC molecules in COOT or in O? It seems there is no
LEGO and TORSION tools for sugar in O. Should I fit them into the
density by rotate and translate each NAC molecule manually?
On Jan 8, 2008 5:37 PM, Laurent Maveyraud <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Hi Jiamu,
just add the desired sugar residue (likely a GlcNAc for a
N-glycosylated
Asn) (ND atom of ASN linked to C1 of sugar. Refmac should handle it
properly. If not you have to add aLINK statement in the PDB
header. Take any
glycosylated structure in the PDB as an example (eg ricin, 2AAI).
Feel free to ask further if needed !
best regards
laurent
-------------------------------------------------------------------
Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr
Université Paul Sabatier Toulouse III
I.P.B.S. UMR 5089 Groupe de Biophysique Structurale
Département Mécanismes Moléculaires des Infections Mycobactériennes
205 route de Narbonne 31077 TOULOUSE Cedex FRANCE
Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994
-------------------------------------------------------------------
________________________________
De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>] De la part de Jiamu
Du
Envoyé : mardi 8 janvier 2008 10:00
À : CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
Objet : [ccp4bb] how to model glycosylated residues?
Dear All:
As mentioned before, I am working on a 2.6 A resolution structure.
There
might be a glycosylated Asn.
I want to model some carbohydrate molecule into my structure.
My question is how to model them? Should I treat them as small
molecules?
Best Regards.
--
Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)
--
Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)
