Grant

You can use the data links that are defined in the Monomer Library (or define them yourself). For example, the alpha 1-2 link is defined below. You need to create a file something like this

refinement.pdb_interpretation.apply_cif_link {
data_link = ALPHA1-2
residue_selection_1 = chain A and resname GAL and resid 1
residue_selection_2 = chain A and resname FUC and resid 2
}

and pass this to phenix.refine. I leave the details to you. You can read the glycosidic bond links in

$PHENIX/chem_data/mon_lib/list/mon_lib_list.cif starting at line 4080.

You can read more about linking at http://phenix-online.org/documentation/refinement.htm#anch78

Nigel

data_link_ALPHA1-2
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
ALPHA1-2 1 O2      2 C1        single       1.439    0.020
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
ALPHA1-2 1 C2      1 O2      2 C1      108.700    3.000
ALPHA1-2 1 O2      2 C1      2 O5      112.300    3.000
ALPHA1-2 1 O2      2 C1      2 C2      109.470    3.000
ALPHA1-2 1 O2      2 C1      2 H1      109.470    3.000
loop_
_chem_link_tor.link_id
_chem_link_tor.id
_chem_link_tor.atom_1_comp_id
_chem_link_tor.atom_id_1
_chem_link_tor.atom_2_comp_id
_chem_link_tor.atom_id_2
_chem_link_tor.atom_3_comp_id
_chem_link_tor.atom_id_3
_chem_link_tor.atom_4_comp_id
_chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
ALPHA1-2 ALPHA_1 1 O2     2 C1     2 C2     2 C3        0.00 20.0 1
ALPHA1-2 ALPHA_2 1 C2     1 O2     2 C1     2 C2        0.00 20.0 1
ALPHA1-2 ALPHA_3 1 C1     1 C2     1 O2     2 C1        0.00 20.0 1
loop_
_chem_link_chir.link_id
_chem_link_chir.atom_centre_comp_id
_chem_link_chir.atom_id_centre
_chem_link_chir.atom_1_comp_id
_chem_link_chir.atom_id_1
_chem_link_chir.atom_2_comp_id
_chem_link_chir.atom_id_2
_chem_link_chir.atom_3_comp_id
_chem_link_chir.atom_id_3
_chem_link_chir.volume_sign
ALPHA1-2   2 C1      1 O2      2 O5      2 C2      negativ

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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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : [email protected]
Fax   : 510-486-5909     Web   : CCI.LBL.gov