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