Error during RNA-Protein Docking

Discussed in https://github.com/RosettaCommons/rosetta/discussions/147

^{Originally posted by kabe89 September 4, 2024}
I am currently trying to extract the pdb files from a silent output file generated by rna_denovo.
the command flags are -minimize_rna false -nstruct 2000 -rna_protein_docking true -cycles 110 -ignore_zero_occupancy false -new_fold_tree_initializer true -convert_protein_CEN false -ramp_rnp_vdw true -bps_moves false -FA_low_res_rnp_scoring true

However, when I run extract_pdbs on this out file, I receive:

ERROR: ambiguous res_num & chain & segid 1
ERROR:: Exit from: src/core/pose/full_model_info/FullModelParameters.cc line: 419

[ ERROR ]: Caught exception:

File: src/core/pose/full_model_info/FullModelParameters.cc:419
[ ERROR ] UtilityExitException
ERROR: ambiguous res_num & chain & segid 1

I run rna_denovo using an RNA sequence on a tetrameric protein PDB file, which has all of the residues renumbered so all of the residues have different numbers. I tried to use the same numbering for all of the chains 1-200, chain A, 1-200, and chain B; however, that resulted in the same issue.
The secondary structure is provided as a combination of all four protein chains and the RNA sequence.
I ran validate_silent
which resulted in
core.io.silent.SilentFileData: Finished reading 2108 structures from OutputfileName.out
pct_good: 1 pct_failed: 0 pct_mismatch: 0

Any help with this matter is greatly appreciated.

Reproduce the failure with rna_denovo and extract_pdbs using the listed flags and tetrameric protein setup. Start at src/core/pose/full_model_info/FullModelParameters.cc:419 and compare the silent-file validation result with extraction; done means identifying the source of the ambiguous residue mapping and making extraction succeed or documenting the required input arrangement.