[phenixbb] histo-blood group antigens

Hansman, Grant (NIH/VRC) [F] hansmang at mail.nih.gov
Tue Apr 20 16:14:17 PDT 2010


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)


refinement.pdb_interpretation {
  apply_cif_link {
    data_link = ALPHA1-2
    residue_selection_1 = chain D and resname GAL and resid 2
    residue_selection_2 = chain D and resname FUC and resid 1
  }
  apply_cif_link {
    data_link = BETA1-3
    residue_selection_1 = chain D and resname NGA and resid 3
    residue_selection_2 = chain D and resname GAL and resid 2



BUT now I have a new sugar (below is the pdb). I want to create the links, does anyone know how to do this?

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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