[phenixbb] How do I make trisaccharide, tetrasaccharides
Pavel Afonine
PAfonine at lbl.gov
Tue Apr 27 20:23:26 PDT 2010
Hi,
it's as easy as 1-2-3 -:) (I hope):
- define custom bonds between corresponding atoms;
- get CIF file (if necessary) (I guess you need it for GLA);
- run phenix.refine without using X-ray term (geometry regularization only),
and that will do exactly what you want. Please let me know if you need
any help with this.
Pavel.
On 4/27/10 4:21 PM, Hansman, Grant (NIH/VRC) [F] wrote:
>
> How do I make trisaccharide, tetrasaccharides, etc from single
> monosaccharides? I.e., how do I join the monosaccharides. Do I use
> ideal coordinates? Can I join them in coot? I want to make HBGA
> Trisaccharide B.
>
>
>
> That is, I want to join FUC-GAL-GLA, it would be FUC (C1)-GAL (O2)-GAL
> (C2) then GAL (C3)-GAL(O3)-GLA(C1)
>
>
>
>
>
>
>
> ATOM 1 C1 FUC A 1 1.410 0.468 -0.410 1.00
> 10.00 C
>
> ATOM 2 C2 FUC A 1 0.120 0.513 -1.233 1.00
> 10.00 C
>
> ATOM 3 C3 FUC A 1 -0.831 -0.576 -0.728 1.00
> 10.00 C
>
> ATOM 4 C4 FUC A 1 -1.016 -0.402 0.783 1.00
> 10.00 C
>
> ATOM 5 C5 FUC A 1 0.359 -0.379 1.454 1.00
> 10.00 C
>
> ATOM 6 C6 FUC A 1 0.185 -0.241 2.967 1.00
> 10.00 C
>
> ATOM 7 O1 FUC A 1 2.007 -0.823 -0.535 1.00
> 10.00 O
>
> ATOM 8 O2 FUC A 1 0.424 0.284 -2.610 1.00
> 10.00 O
>
> ATOM 9 O3 FUC A 1 -2.094 -0.452 -1.385 1.00
> 10.00 O
>
> ATOM 10 O4 FUC A 1 -1.700 0.824 1.044 1.00
> 10.00 O
>
> ATOM 11 O5 FUC A 1 1.116 0.724 0.961 1.00
> 10.00 O
>
>
>
> ATOM 1 C1 GAL A 1 1.384 0.161 -0.445 1.00
> 10.00 C
>
> ATOM 2 C2 GAL A 1 0.328 -0.139 -1.512 1.00
> 10.00 C
>
> ATOM 3 C3 GAL A 1 -0.975 0.575 -1.139 1.00
> 10.00 C
>
> ATOM 4 C4 GAL A 1 -1.360 0.176 0.289 1.00
> 10.00 C
>
> ATOM 5 C5 GAL A 1 -0.177 0.454 1.220 1.00
> 10.00 C
>
> ATOM 6 C6 GAL A 1 -0.563 0.093 2.655 1.00
> 10.00 C
>
> ATOM 7 O1 GAL A 1 2.612 -0.476 -0.802 1.00
> 10.00 O
>
> ATOM 8 O2 GAL A 1 0.785 0.328 -2.782 1.00
> 10.00 O
>
> ATOM 9 O3 GAL A 1 -2.011 0.186 -2.044 1.00
> 10.00 O
>
> ATOM 10 O4 GAL A 1 -1.686 -1.213 0.327 1.00
> 10.00 O
>
> ATOM 11 O5 GAL A 1 0.945 -0.328 0.819 1.00
> 10.00 O
>
> ATOM 12 O6 GAL A 1 0.539 0.355 3.526 1.00
> 10.00 O
>
>
>
> ATOM 1 C1 GLA A 1 1.424 -0.489 -0.382 1.00
> 10.00 C
>
> ATOM 2 C2 GLA A 1 0.392 -0.498 -1.512 1.00
> 10.00 C
>
> ATOM 3 C3 GLA A 1 -0.650 0.592 -1.244 1.00
> 10.00 C
>
> ATOM 4 C4 GLA A 1 -1.222 0.387 0.163 1.00
> 10.00 C
>
> ATOM 5 C5 GLA A 1 -0.068 0.330 1.166 1.00
> 10.00 C
>
> ATOM 6 C6 GLA A 1 -0.630 0.161 2.579 1.00
> 10.00 C
>
> ATOM 7 O1 GLA A 1 2.043 0.797 -0.316 1.00
> 10.00 O
>
> ATOM 8 O2 GLA A 1 1.044 -0.242 -2.757 1.00
> 10.00 O
>
> ATOM 9 O3 GLA A 1 -1.700 0.498 -2.209 1.00
> 10.00 O
>
> ATOM 10 O4 GLA A 1 -1.958 -0.836 0.206 1.00
> 10.00 O
>
> ATOM 11 O5 GLA A 1 0.783 -0.771 0.859 1.00
> 10.00 O
>
> ATOM 12 O6 GLA A 1 0.446 0.112 3.517 1.00
> 10.00 O
>
> ------------------------------------------------------------------------
>
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