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Grant<br>
<br>
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<br>
<br>
refinement.pdb_interpretation.apply_cif_link {<br>
data_link = ALPHA1-2<br>
residue_selection_1 = chain A and resname GAL and resid 1<br>
residue_selection_2 = chain A and resname FUC and resid 2<br>
}<br>
<br>
and pass this to phenix.refine. I leave the details to you. You can
read the glycosidic bond links in<br>
<br>
$PHENIX/chem_data/mon_lib/list/mon_lib_list.cif starting at line 4080.<br>
<br>
You can read more about linking at
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/refinement.htm#anch78">http://phenix-online.org/documentation/refinement.htm#anch78</a><br>
<br>
Nigel<br>
<br>
data_link_ALPHA1-2<br>
#<br>
loop_<br>
_chem_link_bond.link_id<br>
_chem_link_bond.atom_1_comp_id<br>
_chem_link_bond.atom_id_1<br>
_chem_link_bond.atom_2_comp_id<br>
_chem_link_bond.atom_id_2<br>
_chem_link_bond.type<br>
_chem_link_bond.value_dist<br>
_chem_link_bond.value_dist_esd<br>
ALPHA1-2 1 O2 2 C1 single 1.439 0.020<br>
loop_<br>
_chem_link_angle.link_id<br>
_chem_link_angle.atom_1_comp_id<br>
_chem_link_angle.atom_id_1<br>
_chem_link_angle.atom_2_comp_id<br>
_chem_link_angle.atom_id_2<br>
_chem_link_angle.atom_3_comp_id<br>
_chem_link_angle.atom_id_3<br>
_chem_link_angle.value_angle<br>
_chem_link_angle.value_angle_esd<br>
ALPHA1-2 1 C2 1 O2 2 C1 108.700 3.000<br>
ALPHA1-2 1 O2 2 C1 2 O5 112.300 3.000<br>
ALPHA1-2 1 O2 2 C1 2 C2 109.470 3.000<br>
ALPHA1-2 1 O2 2 C1 2 H1 109.470 3.000<br>
loop_<br>
_chem_link_tor.link_id<br>
_chem_link_tor.id<br>
_chem_link_tor.atom_1_comp_id<br>
_chem_link_tor.atom_id_1<br>
_chem_link_tor.atom_2_comp_id<br>
_chem_link_tor.atom_id_2<br>
_chem_link_tor.atom_3_comp_id<br>
_chem_link_tor.atom_id_3<br>
_chem_link_tor.atom_4_comp_id<br>
_chem_link_tor.atom_id_4<br>
_chem_link_tor.value_angle<br>
_chem_link_tor.value_angle_esd<br>
_chem_link_tor.period<br>
ALPHA1-2 ALPHA_1 1 O2 2 C1 2 C2 2 C3 0.00 20.0 1<br>
ALPHA1-2 ALPHA_2 1 C2 1 O2 2 C1 2 C2 0.00 20.0 1<br>
ALPHA1-2 ALPHA_3 1 C1 1 C2 1 O2 2 C1 0.00 20.0 1<br>
loop_<br>
_chem_link_chir.link_id<br>
_chem_link_chir.atom_centre_comp_id<br>
_chem_link_chir.atom_id_centre<br>
_chem_link_chir.atom_1_comp_id<br>
_chem_link_chir.atom_id_1<br>
_chem_link_chir.atom_2_comp_id<br>
_chem_link_chir.atom_id_2<br>
_chem_link_chir.atom_3_comp_id<br>
_chem_link_chir.atom_id_3<br>
_chem_link_chir.volume_sign<br>
ALPHA1-2 2 C1 1 O2 2 O5 2 C2 negativ<br>
<br>
On 4/27/10 4:21 PM, Hansman, Grant (NIH/VRC) [F] wrote:
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<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 1 C1
FUC A 1 1.410
0.468 -0.410 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 2 C2
FUC A 1 0.120
0.513 -1.233 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 3 C3
FUC A 1 -0.831 -0.576
-0.728 1.00 10.00
C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 4 C4
FUC A 1 -1.016
-0.402 0.783 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 5 C5
FUC A 1 0.359
-0.379 1.454 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 6 C6
FUC A 1 0.185
-0.241 2.967 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 7 O1
FUC A 1 2.007
-0.823 -0.535 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 8 O2
FUC A 1 0.424
0.284 -2.610 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 9 O3
FUC A 1 -2.094 -0.452
-1.385 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 10 O4
FUC
A 1 -1.700
0.824 1.044 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Courier New";">ATOM
11 O5 FUC A 1
1.116 0.724 0.961 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Courier New";"><o:p> </o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 1 C1
GAL A 1 1.384
0.161 -0.445 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 2 C2
GAL A 1 0.328 -0.139
-1.512 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 3 C3
GAL A 1 -0.975
0.575 -1.139 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 4 C4
GAL A 1 -1.360
0.176 0.289 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 5 C5
GAL A 1 -0.177
0.454 1.220 1.00 10.00
C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 6 C6
GAL A 1 -0.563
0.093 2.655 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 7 O1
GAL A 1 2.612
-0.476 -0.802 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 8 O2
GAL A 1 0.785
0.328 -2.782 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 9 O3
GAL A 1 -2.011
0.186 -2.044 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 10 O4
GAL
A 1 -1.686 -1.213
0.327 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 11 O5
GAL
A 1 0.945
-0.328 0.819 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Courier New";">ATOM
12 O6 GAL A 1
0.539 0.355 3.526 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Courier New";"><o:p> </o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 1 C1
GLA A 1 1.424
-0.489 -0.382 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 2 C2
GLA A 1 0.392
-0.498 -1.512 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 3 C3
GLA A 1 -0.650 0.592
-1.244 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 4 C4
GLA A 1 -1.222
0.387 0.163 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 5 C5
GLA A 1 -0.068
0.330 1.166 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 6 C6
GLA A 1 -0.630
0.161 2.579 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 7 O1
GLA A 1 2.043
0.797 -0.316 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 8 O2
GLA A 1 1.044
-0.242 -2.757 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 9 O3
GLA A 1 -1.700
0.498 -2.209 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 10 O4
GLA
A 1 -1.958 -0.836
0.206 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 11 O5
GLA
A 1 0.783
-0.771 0.859 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Courier New";">ATOM
12 O6 GLA A 1
0.446 0.112 3.517 1.00
10.00 O</span><o:p></o:p></p>
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<pre class="moz-signature" cols="72">--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Fax : 510-486-5909 Web : CCI.LBL.gov</pre>
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