5
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Lets say you have two times the same molecule in PDB format.

PDB1:

HETATM 1916  C1  EQU A1128      22.568 -34.213 -37.632  1.00 19.82           C
HETATM 1917  O1  EQU A1128      21.807 -35.267 -37.474  1.00 17.07           O
HETATM 1918  C2  EQU A1128      22.218 -33.078 -36.885  1.00 19.81           C
HETATM 1919  C3  EQU A1128      23.024 -31.912 -37.017  1.00 21.42           C
HETATM 1920  C4  EQU A1128      24.206 -31.909 -37.929  1.00 24.79           C
HETATM 1921  C5  EQU A1128      24.504 -33.085 -38.661  1.00 20.61           C
HETATM 1922  C6  EQU A1128      23.703 -34.217 -38.516  1.00 17.92           C
HETATM 1923  C10 EQU A1128      22.658 -30.748 -36.242  1.00 22.26           C
HETATM 1924  C11 EQU A1128      23.461 -29.573 -36.367  1.00 21.01           C
HETATM 1925  C12 EQU A1128      24.609 -29.558 -37.249  1.00 24.75           C
HETATM 1926  C13 EQU A1128      24.992 -30.715 -38.034  1.00 24.09           C
HETATM 1927  C16 EQU A1128      25.402 -28.301 -37.351  1.00 23.63           C
HETATM 1928  C17 EQU A1128      26.110 -28.153 -38.728  1.00 25.12           C
HETATM 1929  C18 EQU A1128      26.990 -29.384 -39.036  1.00 23.20           C
HETATM 1930  C19 EQU A1128      26.187 -30.715 -38.965  1.00 23.69           C
HETATM 1931  C24 EQU A1128      24.645 -26.944 -37.282  1.00 25.63           C
HETATM 1932  C25 EQU A1128      25.847 -25.958 -37.473  1.00 24.96           C
HETATM 1933  C26 EQU A1128      26.770 -26.799 -38.426  1.00 26.13           C
HETATM 1934  O26 EQU A1128      27.843 -26.441 -38.854  1.00 29.46           O
HETATM 1935  C27 EQU A1128      25.111 -27.931 -39.875  1.00 24.05           C

PDB2:

HETATM    1  C10 LIG     1      22.735 -30.818 -36.280  1.00  0.00           C
HETATM    2  C5  LIG     1      24.497 -33.076 -38.614  1.00  0.00           C
HETATM    3  C11 LIG     1      23.469 -29.649 -36.412  1.00  0.00           C
HETATM    4  C6  LIG     1      23.704 -34.219 -38.496  1.00  0.00           C
HETATM    5  C2  LIG     1      22.306 -33.076 -36.899  1.00  0.00           C
HETATM    6  C3  LIG     1      23.085 -31.931 -37.022  1.00  0.00           C
HETATM    7  C4  LIG     1      24.186 -31.919 -37.892  1.00  0.00           C
HETATM    8  C12 LIG     1      24.550 -29.604 -37.290  1.00  0.00           C
HETATM    9  C13 LIG     1      24.951 -30.740 -38.009  1.00  0.00           C
HETATM   10  C1  LIG     1      22.602 -34.190 -37.652  1.00  0.00           C
HETATM   11  C26 LIG     1      26.758 -26.817 -38.473  1.00  0.00           C
HETATM   12  C19 LIG     1      26.180 -30.692 -38.934  1.00  0.00           C
HETATM   13  C25 LIG     1      25.881 -26.016 -37.526  1.00  0.00           C
HETATM   14  C18 LIG     1      27.001 -29.371 -38.996  1.00  0.00           C
HETATM   15  C24 LIG     1      24.709 -26.963 -37.185  1.00  0.00           C
HETATM   16  C16 LIG     1      25.367 -28.337 -37.396  1.00  0.00           C
HETATM   17  C17 LIG     1      26.086 -28.150 -38.747  1.00  0.00           C
HETATM   18  C27 LIG     1      25.093 -27.987 -39.938  1.00  0.00           C
HETATM   19  O26 LIG     1      27.821 -26.440 -38.923  1.00  0.00           O
HETATM   20  O1  LIG     1      21.738 -35.208 -37.538  1.00  0.00           O

In the third column you can see the atom names (C1, O20, etc.). They are different for both PDB files even though it is the same molecule. I would like them to have the same names for the same atoms. So instead of C13 and C9 I would like to have them both named C13 or C9.

What is the convention to name these atoms? What method should I use to convert them to a common naming?

ps. I left out most of the PDB to save space

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You'd need to have some sort of ligand dictionary. For many PDB ligands, this exists, and you can look up the atom naming.

For example, the PDB ligand expo allow you to search for ligands by 3-letter code (e.g., HEM).

The PDBeChem also lets you find atom names based on 3-letter codes (the link is HEM).

However, as far as I know, there isn't (yet) any sort of pattern matching that would allow you to go through PDB files and automatically perceive your ligands, sort the atoms, and name them systematically.

If you find one, please let me know - it would be a great addition to programs like Open Babel

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The convention for the canonical atoms names can be found in the Chemical Component Dictionary (CCD). As for the method, I would use the Vim method of deleting and pasting lines. Another fancy way would be to use a graph approach based on element and do a matching on a per node basis. This would be an excellent Master thesis project, to develop such a fine piece of software.

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