Thank you for your help. I have make my CNS work on the structure refine
successfully.
Best Regards.
On Jan 10, 2008 4:51 AM, Li Zhijie <[log in to unmask]> wrote:
> Hi Jiamu,
>
> I think the glycoside linkages are specified in the generate.inp file.
> The text I list in the end of this email is taken from my generate.inp for
> a structure with (man)3Gn (the tri-mannose core plus a 1.3 arm GlcNAc, not
> the two core GlcNAc):
> (GlcNAc)-b12-(Man)-a13-(Man)-a16-(Man). The numbering is 4-3-2-1 in the
> same order.
>
> The "C" in segid means they are 4 residues in the "C" chain. And the sugar
> giving reducing end is the "-", or, the "carbo_i".
>
>
> I think the N-linkage between a GlcNAc and an Asn is the same thing - but
> I've never really tried. However the default generate.inp seems to already
> have two N-linked entrys (the "B1N"), you just need to specify the residues
> and change the "false" to "true".
>
> I did mine some time ago. Not sure if that is all you need to do. Please
> let know if it works.
>
>
> {=========================== carbohydrate links
> ===========================}
>
> {* Select pairs of residues that are linked *}
> {* First entry is the name of the patch residue. *}
> {* Second and third entries are the resid and segid for the atoms
> referenced by "-" in the patch. *}
> {* Fourth and fifth entries are the resid and segid for the atoms
> referenced by "+" in the patch *}
> {+ table: rows=6 numbered
> cols=6 "use" "patch name" "segid -" "resid -" "segid +" "resid
> +" +}
>
> {+ choice: true false +}
> {===>} carbo_use_1=true;
> {===>} carbo_patch_1="A16";
> {===>} carbo_i_segid_1="C"; carbo_i_resid_1=1;
> {===>} carbo_j_segid_1="C"; carbo_j_resid_1=2;
>
> {+ choice: true false +}
> {===>} carbo_use_2=true;
> {===>} carbo_patch_2="A13";
> {===>} carbo_i_segid_2="C"; carbo_i_resid_2=3;
> {===>} carbo_j_segid_2="C"; carbo_j_resid_2=2;
>
> {+ choice: true false +}
> {===>} carbo_use_3=true;
> {===>} carbo_patch_3="B12";
> {===>} carbo_i_segid_3="C"; carbo_i_resid_3=4;
> {===>} carbo_j_segid_3="C"; carbo_j_resid_3=3;
>
>
>
> {========================= generate parameters
> =============================}
>
> ----- Original Message -----
> *From:* Jiamu Du <[log in to unmask]>
> *To:* [log in to unmask]
> *Sent:* Wednesday, January 09, 2008 4:14 AM
> *Subject:* Re: [ccp4bb] how to model glycosylated residues?
>
> Dear All,
> Thank you for your previous response. I have built a 3-mer oligosaccharides
> in the electron density by using coot. I prefer to refine my structure in
> CNS due the resolution is only 2.6 Ang. I found there are only topology
> and parameter files for carbohydrate in CNS but no linkage file for
> carbohydrate. So CNS could recognize the sugar molecules individually, but
> can not recognize the linkage between them. When I refine it in CNS, a
> oxygen will be added beyond C1 of NAG.
> Is there anyone who has the linkage file for carbohydrate of CNS? Or is
> there any other methods to deal with this situation?
>
> Thanks.
>
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>
--
Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)
