[MMTK] Connectivity of hetero groups in PDB files

bgbg bg bgbg.bg at gmail.com
Fri Aug 8 11:24:09 UTC 2008


Hello.
I cannot figure out how to preserve the connectivity of hetero groups
in PDB files. The following example shows loading the 4DFR complex and
saving one of the metotrexate molecules to a file. As you can see, no
CONECT entries are available.
Can anyone help me?


In [14]: import MMTK

In [15]: dfr=MMTK.PDB.PDBFile('4DFR.pdb')

In [16]: mtx=dfr.molecules['MTX'][0]

In [17]: mtx.writeToFile('mtx.pdb')

In [18]: _ip.system("cat mtx.pdb")
HETATM    1  N1  MTX     1       2.298   5.867   2.449  1.00  0.15           N
HETATM    2  C2  MTX     1       2.347   5.821   2.328  1.00  0.17           C
HETATM    3  NA2 MTX     1       2.480   5.822   2.321  1.00  0.16           N
HETATM    4  N3  MTX     1       2.279   5.782   2.223  1.00  0.18           N
HETATM    5  C4  MTX     1       2.146   5.780   2.207  1.00  0.19           C
HETATM    6  NA4 MTX     1       2.082   5.744   2.107  1.00  0.18           N
HETATM    7  C4A MTX     1       2.090   5.830   2.336  1.00  0.19           C
HETATM    8  N5  MTX     1       1.956   5.851   2.337  1.00  0.20           N
HETATM    9  C6  MTX     1       1.899   5.898   2.442  1.00  0.19           C
HETATM   10  C7  MTX     1       1.978   5.926   2.563  1.00  0.19           C
HETATM   11  N8  MTX     1       2.110   5.918   2.556  1.00  0.22           N
HETATM   12  C8A MTX     1       2.161   5.859   2.436  1.00  0.19           C
HETATM   13  C9  MTX     1       1.746   5.901   2.445  1.00  0.20           C
HETATM   14  N10 MTX     1       1.696   5.997   2.553  1.00  0.17           N
HETATM   15  CM  MTX     1       1.623   5.918   2.664  1.00  0.22           C
HETATM   16  C11 MTX     1       1.812   6.410   2.580  1.00  0.22           C
HETATM   17  C12 MTX     1       1.729   6.351   2.673  1.00  0.19           C
HETATM   18  C13 MTX     1       1.684   6.219   2.669  1.00  0.18           C
HETATM   19  C14 MTX     1       1.732   6.145   2.568  1.00  0.20           C
HETATM   20  C15 MTX     1       1.814   6.210   2.467  1.00  0.18           C
HETATM   21  C16 MTX     1       1.852   6.341   2.474  1.00  0.17           C
HETATM   22  C   MTX     1       1.819   6.563   2.583  1.00  0.23           C
HETATM   23  O   MTX     1       1.752   6.628   2.678  1.00  0.26           O
HETATM   24  N   MTX     1       1.933   6.598   2.514  1.00  0.21           N
HETATM   25  CA  MTX     1       1.984   6.746   2.514  1.00  0.23           C
HETATM   26  CT  MTX     1       2.016   6.755   2.364  1.00  0.23           C
HETATM   27  O1  MTX     1       2.029   6.666   2.285  1.00  0.21           O
HETATM   28  O2  MTX     1       1.992   6.875   2.315  1.00  0.27           O
HETATM   29  CB  MTX     1       2.122   6.767   2.576  1.00  0.27           C
HETATM   30  CG  MTX     1       2.089   6.764   2.732  1.00  0.36           C
HETATM   31  CD  MTX     1       1.992   6.852   2.836  1.00  0.41           C
HETATM   32  OE1 MTX     1       1.941   6.837   2.959  1.00  0.49           O
HETATM   33  OE2 MTX     1       1.944   6.947   2.749  1.00  0.42           O
END



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