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<p class=MsoNormal>I want to add a trisaccharide to my structure, but when I
run phenix.refine the sugar breaks up. I know I need to specify the links on
the sugar and that they must be in the reverse order, but I don’t know
how to do that.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>i.e., Some thing like this… which worked fine with a
different sugar (below) <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='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>refinement.pdb_interpretation {<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> data_link = ALPHA1-2<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> residue_selection_1 = chain D and
resname GAL and resid 2<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> residue_selection_2 = chain D and
resname FUC and resid 1<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> }<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> apply_cif_link {<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> data_link = BETA1-3<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> residue_selection_1 = chain D and
resname NGA and resid 3<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>
residue_selection_2 = chain D and resname GAL and resid 2<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>BUT
</span>now I have a new sugar (below is the pdb). I want to create the links,
does anyone know how to do this?<span style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2386 C1 FUC A
1 16.834 10.319 -8.554 1.00
66.42 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2387 C2 FUC A
1 16.606 11.012 -7.166 1.00
61.84 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2388 C3 FUC A
1 17.009 12.513 -7.241 1.00
59.45 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2389 C4 FUC A
1 16.144 13.200 -8.308 1.00
60.73 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2390 C5 FUC A
1 16.343 12.478 -9.659 1.00
61.11 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2391 C6 FUC A
1 15.451 13.074 -10.752 1.00
58.85 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2392 O1 FUC A
1 18.293 10.173 -8.848 1.00
75.63 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2393 O2 FUC A
1 17.360 10.357 -6.166 1.00
60.01 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2394 O3 FUC A
1 16.815 13.162 -5.990 1.00
59.75 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2395 O4 FUC A
1 14.774 13.159 -7.919 1.00
58.98 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2396 O5 FUC A
1 16.051 11.063 -9.520 1.00
61.98 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2397 C1 GAL A
2 18.717 9.760 -11.037 1.00
85.92 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2398 C2 GAL A
2 18.373 9.162 -9.615
1.00 83.98 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2399 C3 GAL A
2 19.592 8.289 -9.187
1.00 87.51 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2400 C4 GAL A 2
19.814 7.192 -10.269 1.00
87.23 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2401 C5 GAL A
2 20.123 7.872 -11.635 1.00
86.28 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2402 C6 GAL A
2 20.336 6.876 -12.795 1.00
83.95 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2403 O2 GAL A
2 17.629 10.430 -11.635 1.00
91.09 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2404 O3 GAL A
2 18.638 6.383 -10.380 1.00
88.24 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2405 O4 GAL A
2 19.031 8.744 -12.000 1.00
86.74 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2406 O5 GAL A
2 20.641 7.401 -14.059 1.00
79.17 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2407 O6 GAL A
2 20.370 8.579 -8.053
1.00 95.12 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2408 C1 NGA A
3 20.960 9.184 -6.913
1.00100.54 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2409 C2 NGA A
3 20.707 8.446 -5.548
1.00103.23 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2410 C3 NGA A
3 20.064 9.437 -4.546
1.00103.55 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2411 C4 NGA A
3 21.015 10.661 -4.359
1.00103.72 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2412 C5 NGA A
3 21.252 11.342 -5.751
1.00103.24 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2413 C6 NGA A
3 22.221 12.560 -5.693
1.00103.28 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2414 C7 NGA A
3 20.349 6.053 -6.269
1.00107.39 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2415 C8 NGA A 3
19.294 4.961 -6.441
1.00107.38 C <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2416 N2 NGA A
3 19.860 7.256 -5.781
1.00105.47 N <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2417 O3 NGA A
3 19.829 8.805 -3.291
1.00102.40 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2418 O4 NGA A
3 22.255 10.230 -3.783
1.00105.38 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2419 O5 NGA A
3 21.766 10.375 -6.714
1.00101.87 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2420 O6 NGA A
3 22.993 12.697 -6.878
1.00104.86 O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>HETATM 2421 O7 NGA A
3 21.514 5.860 -6.552
1.00110.32
O <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>END
<o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Kindly,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Grant<o:p></o:p></p>
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