[phenixbb] histo-blood group antigens

[Edward A. Berry]

Hansman, Grant (NIH/VRC) [F] wrote:
> 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.
>
> i.e., Some thing like this… which worked fine with a different sugar
> (below)
 . .
>
> BUT now I have a new sugar (below is the pdb). I want to create the
> links, does anyone know how to do this?
>

Maybe refine.geometry_restraints.edits {}

Find the following in .eff or .def and edit:

   geometry_restraints.edits {
     excessive_bond_distance_limit = 10
     bond {
       action = *add delete change
       atom_selection_1 = None
       atom_selection_2 = None
       symmetry_operation = None
       distance_ideal = None
       sigma = None
       slack = None
     }
 . .
   }

(duplicate the bond{} as needed)
atom selection syntax:
  atom_selection_1 = chain D and resname CYS and resid 101 and name SG
  atom_selection_2 = chain D and resname HEC and resid 4003 and name CAB


> HETATM 2386 C1 FUC A 1 16.834 10.319 -8.554 1.00 66.42 C
>
> HETATM 2387 C2 FUC A 1 16.606 11.012 -7.166 1.00 61.84 C
>
> HETATM 2388 C3 FUC A 1 17.009 12.513 -7.241 1.00 59.45 C
>
> HETATM 2389 C4 FUC A 1 16.144 13.200 -8.308 1.00 60.73 C
>
> HETATM 2390 C5 FUC A 1 16.343 12.478 -9.659 1.00 61.11 C
>
> HETATM 2391 C6 FUC A 1 15.451 13.074 -10.752 1.00 58.85 C
>
> HETATM 2392 O1 FUC A 1 18.293 10.173 -8.848 1.00 75.63 O
>
> HETATM 2393 O2 FUC A 1 17.360 10.357 -6.166 1.00 60.01 O
>
> HETATM 2394 O3 FUC A 1 16.815 13.162 -5.990 1.00 59.75 O
>
> HETATM 2395 O4 FUC A 1 14.774 13.159 -7.919 1.00 58.98 O
>
> HETATM 2396 O5 FUC A 1 16.051 11.063 -9.520 1.00 61.98 O
>
> HETATM 2397 C1 GAL A 2 18.717 9.760 -11.037 1.00 85.92 C
>
> HETATM 2398 C2 GAL A 2 18.373 9.162 -9.615 1.00 83.98 C
>
> HETATM 2399 C3 GAL A 2 19.592 8.289 -9.187 1.00 87.51 C
>
> HETATM 2400 C4 GAL A 2 19.814 7.192 -10.269 1.00 87.23 C
>
> HETATM 2401 C5 GAL A 2 20.123 7.872 -11.635 1.00 86.28 C
>
> HETATM 2402 C6 GAL A 2 20.336 6.876 -12.795 1.00 83.95 C
>
> HETATM 2403 O2 GAL A 2 17.629 10.430 -11.635 1.00 91.09 O
>
> HETATM 2404 O3 GAL A 2 18.638 6.383 -10.380 1.00 88.24 O
>
> HETATM 2405 O4 GAL A 2 19.031 8.744 -12.000 1.00 86.74 O
>
> HETATM 2406 O5 GAL A 2 20.641 7.401 -14.059 1.00 79.17 O
>
> HETATM 2407 O6 GAL A 2 20.370 8.579 -8.053 1.00 95.12 O
>
> HETATM 2408 C1 NGA A 3 20.960 9.184 -6.913 1.00100.54 C
>
> HETATM 2409 C2 NGA A 3 20.707 8.446 -5.548 1.00103.23 C
>
> HETATM 2410 C3 NGA A 3 20.064 9.437 -4.546 1.00103.55 C
>
> HETATM 2411 C4 NGA A 3 21.015 10.661 -4.359 1.00103.72 C
>
> HETATM 2412 C5 NGA A 3 21.252 11.342 -5.751 1.00103.24 C
>
> HETATM 2413 C6 NGA A 3 22.221 12.560 -5.693 1.00103.28 C
>
> HETATM 2414 C7 NGA A 3 20.349 6.053 -6.269 1.00107.39 C
>
> HETATM 2415 C8 NGA A 3 19.294 4.961 -6.441 1.00107.38 C
>
> HETATM 2416 N2 NGA A 3 19.860 7.256 -5.781 1.00105.47 N
>
> HETATM 2417 O3 NGA A 3 19.829 8.805 -3.291 1.00102.40 O
>
> HETATM 2418 O4 NGA A 3 22.255 10.230 -3.783 1.00105.38 O
>
> HETATM 2419 O5 NGA A 3 21.766 10.375 -6.714 1.00101.87 O
>
> HETATM 2420 O6 NGA A 3 22.993 12.697 -6.878 1.00104.86 O
>
> HETATM 2421 O7 NGA A 3 21.514 5.860 -6.552 1.00110.32 O
>
> END
>
> Kindly,
>
> Grant
>
>
>
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