PyMOL+

Overview

Fast batch stills of predicted structures.
Presentation and documentation renders with chain, ligand, or residue highlighting.
Optional video output when a selected mode needs frame-by-frame structure review.

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 still PNG or multi-view PNG from a structure.
`batch_stills` Batch Stills	Consumes a folder or output set; useful for batches and pipeline handoffs.	Render all supported structures in the selected source as stills.
`turntable_animation` Turntable Animation	Consumes a folder or output set; useful for batches and pipeline handoffs.	Render video outputs for structures in the selected source.
`trajectory_animation` Trajectory Animation	Uses one selected file/source when file parameters are present.	Render a video through the states of a multi-state structure.

Canonical Job Configuration

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

Parameter	Type	Modes	What it does
`structure` Structure	Structure file	Still Image, Trajectory Animation	Choose a molecular structure file. Required; Files: .pdb, .ent, .pqr, .cif, .mmcif, .mmtf, .mol2, .sdf
`background` Background	Text	All modes	Background color for images and video frames. Default: Black; Options: Black, White, Transparent
`resolution` Resolution	Integer	All modes	Pixel width/height per rendered tile. Default: 768; Range: 256-2048
`layers` Layers	Repeatable group	All modes	Add one or more visual layers. Select residues in the structure preview, then use them as a layer selector. Required; Default: [{"color":"By Chain","representation":"Cartoon","selector":"all"}]; Items: 1-12
`layers.selector` Selector	Text	All modes	PyMOL selector or a residue selector. Examples: all, chain A, resn ZN, organic, or A10,A12-20. Required
`layers.representation` Representation	Text	All modes	Default: Cartoon; Options: Cartoon, Spheres, Sticks, Surface, Lines, Mesh, Dots
`layers.color` Color	Text	All modes	Default: By Chain; Options: By Chain, By Element, Gray, Gray70, Marine, Cyan, Green, Limegreen, Yellow, Orange, Red, Blue, Magenta, White, Black
`view_count` Views	Integer	Still Image	Set above 1 to render a multi-view still-image collage. Default: 1; Range: 1-12
`batch_rows` Batch Rows	Integer	Batch Stills, Turntable Animation	Rows in each batch collage. Default: 1; Range: 1-4
`batch_cols` Batch Columns	Integer	Batch Stills, Turntable Animation	Columns in each batch collage. Default: 1; Range: 1-4
`batch_order` Batch Order	Text	Batch Stills, Turntable Animation	Whether to render structures in folder order or randomize selection. Default: Folder Order; Options: Folder Order, Random Sample
`batch_limit` Max Batch Outputs	Integer	Batch Stills, Turntable Animation	Maximum number of batch outputs to produce. Leave empty for all. Range: 0-100
`animation_smoothness` Smoothness	Text	Turntable Animation	Higher smoothness produces more frames and larger outputs. Default: Standard; Options: Preview, Standard, Smooth
`animation_speed` Playback Speed	Text	Turntable Animation, Trajectory Animation	Playback speed for generated videos. Default: Standard; Options: Slow, Standard, Fast
`tile_label_mode` Tile Labels	Text	All modes	Optional label text drawn on each rendered tile. Default: None; Options: None, Sequential Letters, Sequential Numbers, Structure Name, Custom Text
`tile_label_text` Label Text	Text	All modes	Text used when Tile Labels is Custom Text. Shown when tile_label_mode is Custom Text
`tile_label_position` Label Placement	Text	All modes	Default: Top; Options: Top, Bottom; Shown when tile_label_mode is one of Sequential Letters, Sequential Numbers, Structure Name, Custom Text
`tile_label_size` Label Size	Text	All modes	Default: Medium; Options: Small, Medium, Large; Shown when tile_label_mode is one of Sequential Letters, Sequential Numbers, Structure Name, Custom Text
`tile_label_color` Label Color	Text	All modes	Default: White; Options: White, Black, Yellow, Cyan, Magenta, Orange, Limegreen; Shown when tile_label_mode is one of Sequential Letters, Sequential Numbers, Structure Name, Custom Text
`video_format` Video Format	Text	Turntable Animation, Trajectory Animation	Default: MP4; Options: MP4, WebM
`use_preview_orientation` Use Preview Orientation	Yes/no	Still Image	For still images, render from the current structure preview orientation when submitted from the web UI. Default: false

Advanced configuration fields

Parameter	Type	Modes	What it does
`representation` Base Representation	Text	All modes	Legacy base representation used when no layers are supplied. Default: Cartoon; Options: Cartoon, Spheres, Sticks, Surface, Lines, Mesh, Dots
`color_scheme` Base Coloring	Text	All modes	Legacy coloring preset used when no layers are supplied. Default: Default; Options: Default, By Element, By Chain, Chain Rainbow, Secondary Structure, Single Color
`single_color` Single Color	Text	All modes	Color used when the single-color preset is selected. Default: Marine; Options: Marine, Cyan, Green, Yellow, Orange, Red, Blue, Magenta, White; Shown when color_scheme is Single Color
`batch_layout` Legacy Batch Layout	Text	Batch Stills, Turntable Animation	Legacy layout option used only when rows and columns are omitted by older clients. Default: One Per Output; Options: One Per Output, Four Per Output, Six Per Output, Nine Per Output
`reverse_playback` Reverse Playback	Yes/no	Turntable Animation, Trajectory Animation	Reverse angle or state order in the video output. Default: false
`preview_orientation` Preview Orientation	Text	Still Image	Auto-filled by the web UI when using preview orientation. Shown when use_preview_orientation is true
`camera_distance` Camera Distance	Number	All modes	Optional camera zoom distance override. Leave empty for PyMOL+ defaults. Range: 0.1-1000

Outputs And Metrics

PNG still images, videos, and optional PyMOL session/script artifacts depending on mode.
This is a visualization job and does not compute scientific confidence or validation metrics.

Common Examples

Batch stills: select a folder of PDB/CIF files, cartoon representation, chain coloring.
Binding-site figure: add a ligand layer and a residue-selection layer around the pocket.
Structure review video: one structure, consistent camera, MP4 output for sharing.

Example API params

{
  "mode": "still_image",
  "structure": "model.pdb",
  "representation": "Cartoon",
  "color_scheme": "By Chain"
}

Caveats

Selections must match chains, residue names, and numbering in the input structures.
Large structures and video modes can produce large outputs.
Visualization quality does not imply model quality.

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 accepts one flag per line for lower-level render, batch, and video workflows.
Use canonical configuration when layer-based structure rendering is enough.

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=pymolplus \
  -F 'params={"mode":"single_still","structure":"model.pdb","representation":"cartoon","color_scheme":"chain"}'