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.
By default, the CONECT lines are optional for standard amino acids. (And are strictly not necessary for non-amino acid residues).
If you do need all the CONECT records for a downstream application, use the command line option `-write_all_connect_info`. (You can pass command line options when you call init() - there's ways to control it on a case-by-case basis with the StructFileRepOptions class, but the Pose.dump_pdb() convenience function doesn't expose that.
There's other, similar options which you can control from the command line options: https://new.rosettacommons.org/docs/latest/full-options-list#inout
Thank you very much! That is exactly, what I was looking for.