pdb2pqr does not remove atoms as expected #392
Description
Dear developers,
I am writing python code with pdb2pqr package, and I found that if I created a biomolecule include nucleic acids (PDB ID: 3AU6), calling biomolecule.set_termini() will remove the atom P of residue DG (chain T, residue index 2), but the atoms OP1/OP2 were kept.
This may break the nucleic acid residue and cause more problems.
Python code
from pdb2pqr import io
from pdb2pqr.main import setup_molecule
pdb_file = '3AU6.pdb'
pdb_list = io.get_molecule(pdb_file)[0]
definition = io.get_definitions()
biomolecule, definition, ligand = setup_molecule(pdb_list, definition, None)
biomolecule.set_termini()And the pdb file is like this:
...
HETATM 4625 C6 DDG P 7 0.318 -29.896 14.522 1.00 78.77 C
HETATM 4626 O6 DDG P 7 1.470 -30.120 14.970 1.00 78.13 O
HETATM 4627 N1 DDG P 7 -0.537 -29.076 15.136 1.00 79.20 N
HETATM 4628 C2 DDG P 7 -1.771 -28.834 14.656 1.00 79.68 C
HETATM 4629 N2 DDG P 7 -2.564 -27.995 15.371 1.00 80.87 N
HETATM 4630 N3 DDG P 7 -2.262 -29.385 13.515 1.00 78.01 N
HETATM 4631 C4 DDG P 7 -1.500 -30.217 12.808 1.00 77.69 C
TER
ATOM 4632 OP1 DG T 2 16.134 -30.844 17.533 1.00101.02 O
ATOM 4633 OP2 DG T 2 14.316 -29.326 16.552 1.00103.39 O
ATOM 4634 O5' DG T 2 14.745 -29.259 19.007 1.00101.37 O
ATOM 4635 C5' DG T 2 15.093 -28.069 19.788 1.00100.31 C
ATOM 4636 C4' DG T 2 14.016 -26.980 19.897 1.00 99.38 C
ATOM 4637 O4' DG T 2 13.901 -26.265 18.634 1.00 99.16 O
ATOM 4638 C3' DG T 2 12.588 -27.455 20.191 1.00 98.70 C
ATOM 4639 O3' DG T 2 11.709 -26.388 20.617 1.00 97.61 O
...
This residue also looks broken in pymol:
Are atoms OP1/OP2 not being removed as expected?
Thanks very much!