[phenixbb] How do I make trisaccharide, tetrasaccharides

[Hansman, Grant (NIH/VRC) [F]]

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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