I am trying to retrieve residue-specific secondary structure and solvent accessibility related information from a bunch of PDB files using DSSP program from Biopython. However, I am getting a weird warning about some residues having more sidechain atoms than expected. A minimum working code for reproducing the warning for PDB ID: 5PTI is as follows:
from Bio.PDB import * parser = PDBParser(QUIET=True) structure = parser.get_structure(id='struct',file="5pti.pdb") model = structure dssp = DSSP(model,"5pti.pdb")
For this specific PDB ID, for example, the first warning is, "Residue ARG 1 A has 11 instead of expected 7 sidechain atoms". I have checked the number of atoms for all the arginine residues in this PDB file using the following code:
structure = parser.get_structure(id='struct',file="5pti.pdb") model = structure residues = Selection.unfold_entities(model, 'R') count = 0 for idx,residue in enumerate(residues): if residue.get_resname() == "ARG": atoms = Selection.unfold_entities(residue,'A') print(len(atoms),atoms[len(atoms)-1],residue.get_id()) count = count + 1 print(count)
Can someone please point me towards the reason of this warning? Can I ignore it safely for my purpose? Thanks.