# CONECT information for PDB files by raw sequence

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CONECT information for PDB files by raw sequence
#1

Hello,

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.

Thanks,

Fabian

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Wed, 2022-06-22 01:47
Fata

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

Wed, 2022-06-22 11:54
rmoretti

Thank you very much! That is exactly, what I was looking for.

init(silent=True, options="-write_all_connect_info")

Thu, 2022-06-23 05:34
Fata