The ribosome structure (get one, or build your own)

The explicit-ribosome runner (Synthesis on a coarse-grained ribosome) needs a rigid, oriented, truncated, coarse-grained large subunit as its ribosome input — the 4v9d_50S_PtR_5jte_AtR_model_cg_trunc.pdb you see in tutorials/08_csp_cg_ribosome/. (The cylinder runner needs none of this.)

Every such structure is oriented in the tunnel frame: PTC at the origin, exit tunnel on +x, tRNA tails on +y — so the tunnel axis is the X-axis and the radial distance to it is sqrt(y²+z²).

The canonical ribosome

The reference structure is the E. coli 4V9D 50S subunit (with the 5JTE A-site tRNA grafted in), coarse-grained to the O’Brien P/R/BR representation (4 576 beads) and truncated around the exit tunnel: 4v9d_50S_PtR_5jte_AtR_model_cg_trunc.pdb. It is bundled in tutorials/08_csp_cg_ribosome/.

Point the ribosome key of a csp.ini at any such structure — it is a plain path:

pdb_file  = my_protein.pdb
ribosome  = /path/to/4v9d_50S_PtR_5jte_AtR_model_cg_trunc.pdb

Other organisms / building your own

cosmo does not ship a structure-preparation pipeline (or bundle ribosome structures in the package itself). The synthesis subsystem is a port of the sibling topo package, and the two share the same tunnel frame, truncation rule, and CG mapping — so to prepare a ribosome from any PDB deposition (or to use a ready-made yeast / N. crassa / human structure), use topo’s scripted pipeline and its guide:

  • topo’s assets/csp/prepare_ribosome/ — the fetch → orient → coarse-grain → truncate pipeline plus four ready-made organisms (E. coli, S. cerevisiae, N. crassa, H. sapiens).

  • topo’s usage/ribosome_preparation doc page — the ready-made table, per-organism provenance/caveats, and how to re-truncate with your own criteria.

A structure prepared by that pipeline (P/R/BR representation) drops straight into cosmo-csp — the same 4 576-bead file bundled in the tutorial.

Note

Only the P/R/BR rRNA representation is supported. An earlier single-bead-per-nucleotide (cosmo 1-bead) rep existed for the retired cosmo.translation runner; it is not usable by cosmo-csp (the PTC-geometry optimizer needs the P/R/BR tRNA beads) and has been removed.