Beautiful Atoms

Overview

Publication-style protein structure figures from PDB or CIF files.
Ligand, small-molecule, crystal, and atomistic renders.
Visual QC before sharing a model or result bundle.

Modes

Mode	Input shape	When to use it
`still_image` Still Image Default	Uses one selected file/source when file parameters are present.	Render one high-quality PNG from a structure.
`turntable_animation` Turntable Animation	Uses one selected file/source when file parameters are present.	Render a video view from one structure when a static figure is not enough.

Canonical Job Configuration

These are the fields exposed by the default job configuration for batoms. They are also returned by GET /api/v1/program/params?program=batoms and submitted as the params JSON object to POST /api/v1/job/submit.

Parameter	Type	Modes	What it does
`structure` Structure	Structure file	All modes	Choose a structure file. PDB inputs work best with the default ribbon style. Required; Files: .pdb, .ent, .cif, .mmcif, .xyz, .extxyz, .cube, .vasp
`style` Style	Text	All modes	Ribbon is best for typical protein PDB files. Ball-and-stick is the best alternate for small molecules and atomistic structures. Default: Ribbon; Options: Ribbon, Ball-and-Stick, Space-Filling, Stick, Polyhedral
`background` Background	Text	All modes	Default: White; Options: White, Transparent, Gray, Black
`quality` Quality	Text	All modes	Higher quality increases resolution, samples, and animation frames. Default: Standard; Options: Preview, Standard, High
`video_format` Video Format	Text	Turntable Animation	Default: MP4; Options: MP4, WebM
`animation_speed` Playback Speed	Text	Turntable Animation	Default: Standard; Options: Slow, Standard, Fast

Advanced configuration fields

Parameter	Type	Modes	What it does
`show_unit_cell` Show Unit Cell	Yes/no	All modes	Show crystal unit-cell axes when the input contains cell information. Default: false
`save_blend` Save Blender Scene	Yes/no	All modes	Also write a .blend scene file under /outputs/scenes. Default: false

Outputs And Metrics

Still-image jobs produce a PNG render.
Video jobs produce a movie file and rendered frame sequence.
Optional scene export produces an editable scene artifact.
This is a visualization job; it does not produce scientific confidence, docking, or validation scores.

Common Examples

Protein figure: Still Image, Ribbon, white or transparent background, Standard or High quality.
Ligand render: Still Image, Ball-and-Stick, transparent background, High quality.
Crystal snapshot: Polyhedral or Space-Filling with the unit cell enabled.

Example API params

{
  "mode": "still_image",
  "structure": "model.pdb",
  "style": "Ribbon",
  "background": "White",
  "quality": "Standard"
}

Caveats

Ribbon style is intended for proteins; non-protein systems often render better as Ball-and-Stick or Space-Filling.
High quality and video modes increase output size.
Transparent backgrounds are most useful for PNG stills; video transparency support varies by format.

Advanced Submit

Advanced submit is still available for direct program arguments through POST /api/v1/job/submit-advanced. Prefer canonical configuration unless you need exact low-level arguments or are reproducing a known command line.

Advanced submit can pass lower-level rendering flags for batch views, trajectories, and scene export.
Use canonical configuration for standard stills and supported video modes.

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=batoms \
  -F 'params={"mode":"still_image","structure":"model.pdb","style":"Ribbon","background":"White","quality":"Standard"}'