I create a pose from sequence and dump it as PDB:
pep_pose = pyrosetta.pose_from_sequence(sequence, res_type='fa_standard', auto_termini=True) # pep_pose = pyrosetta.Pose() # pyrosetta.rosetta.core.pose.make_pose_from_sequence(pep_pose, sequence, 'fa_standard', auto_termini=True) pep_pose.dump_pdb(pdb_file_path)
As I understood, 'pose_from_sequence' creates a peptide structure by sequence, but what I found was that the PDB file misses the whole CONECT information.
How can I add the CONECTs to the output PDB file? I am still unsure, if the "bound" information is never created or simply not written during the pdb-dump.