Visualizing the synthesis process

A synthesis run — whether an interrupted-and-resumed production run or a short demo — writes the growing chain as many short trajectories, one per residue (and, for Synthesis on a coarse-grained ribosome, three MD sub-stages per residue). Different lengths have different bead counts, so the segments cannot simply be concatenated. The package stitches them into a single VMD-playable movie that grows the chain N→C, and adds the scenery that makes the process legible: the analytic exit tunnel for the cylinder model, or the coarse-grained ribosome for the explicit-ribosome model.

This page covers turning a finished output directory into an interactive VMD movie you can rotate and replay, for both synthesis runners.

Note

Everything below works the same on a resumed run: cosmo-csp-movie reads whatever L_<L>/ segments are present under the output root, so stitch after the final residue completes.

Stitch the movie (cosmo-csp-movie)

cosmo-csp-movie (= python -m cosmo.csp.movie) auto-detects the on-disk layout — the 3-stage CSP layout (<outdir>/L_<L>/traj_s<1,2,3>.dcd) or the flat per-length layout (<outdir>/L_<L>/traj.dcd, used by the cylinder runner) — plus any ejection/ phase, and writes:

<outdir>/movie.psf     # single topology (padded to the final length)
<outdir>/movie.dcd     # all segments back-to-back, in synthesis order
<outdir>/movie.tcl     # a VMD script that loads the movie and grows the chain

The not-yet-synthesized beads are parked at a far sentinel each frame; the generated movie.tcl hides them per frame (the default --park sentinel scheme).

Important

movie.tcl loads movie.psf / movie.dcd (and, for the ribosome model, movie_ribosome.pdb) by basename, so open it from inside the output directory:

cd <outdir> && vmd -e movie.tcl

Running vmd -e <outdir>/movie.tcl from the parent folder loads the scenery but fails to find the trajectory.

Add the model-specific scenery with one flag, described next.

Cylinder tunnel model (cosmo-cylinder)

The cylinder run has no ribosome beads — the exit tunnel is a pure force. Pass the same cylinder.ini that drove the run so the drawn tunnel (bore tube, closed PTC end cap, and the infinite exit-face wall as an annulus whose hole is the bore) matches the forces the chain actually felt.

# Interactive: stitch + draw the tunnel into movie.tcl, then view from the run folder.
cosmo-csp-movie -o synth_out_cyl --tunnel cylinder.ini      # or: python -m cosmo.csp.movie -o synth_out_cyl --tunnel cylinder.ini
cd synth_out_cyl && vmd -e movie.tcl

You see the chain thread the (blue, transparent) bore, the red PTC cap it grows away from, and the grey exit wall it emerges through — then relax once it clears the tunnel. --wall-outer NM sets the drawn exit-wall radius (default: bore radius + 3 nm); the tunnel geometry comes from cosmo.csp.cylinder.tunnel_tcl.

Coarse-grained ribosome model (cosmo-csp)

The explicit-ribosome run synthesizes on a truncated CG ribosome. Overlay it as static scenery by passing that ribosome PDB:

# Interactive: stitch + overlay the ribosome, then view from the run folder.
cosmo-csp-movie -o synth_out_csp --ribosome 4v9d_50S_PtR_5jte_AtR_model_cg_trunc.pdb
cd synth_out_csp && vmd -e movie.tcl        # also uses movie_ribosome.pdb, written alongside

The nascent-only trajectories exclude the ribosome beads; cosmo-csp-movie re-attaches the ribosome as a separate, static molecule and copies it to <outdir>/movie_ribosome.pdb, so the movie is self-contained.

Notes & tips

  • Plain movie. Omit --tunnel / --ribosome for a bare growing-chain movie (no scenery) — useful as a quick check.

  • --prefix renames the output set (<prefix>.{psf,dcd,tcl}); --outname must match the per-segment basename the runner used (default traj).

  • Parking scheme. --park cterm stacks future beads on the C-terminus instead of the far sentinel (no per-frame hiding needed, but leaves a small bead cluster); sentinel (default) is cleaner.

  • Post-synthesis phase. The ejection/ free run is appended automatically when present, so the movie continues past full length into release.

See also