Hi Illimar,
that's because most of your PDBResidueInfo fields are blank, including atom
names, residue numbers, etc.
If you wish to generate a PDB file that can be visualize correctly you need
to copy this information from the existing atoms, e.g.:
new_res_inf =
Hello, all
I have written a script which extracts certain residues from a PDB file, and
writes them out to a new PDB-file.
The script looks like this:
from rdkit import Chem
def create_sub_mol(mol_in, mol_in_conf, bs_atom_list):
"""
Creates a mol of given atoms atoms, e.g. the atoms
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