When more than one peptide is building the protein there are unrealistically long bonds generated for some residues following each other in the PDB file. When parsing a bond should not be set, if the two residues' center of mass are too far away.
Example PDB file for reproduction is 6B3R.
When more than one peptide is building the protein there are unrealistically long bonds generated for some residues following each other in the PDB file. When parsing a bond should not be set, if the two residues' center of mass are too far away.
Example PDB file for reproduction is 6B3R.