PyMOL+

Workflow

• Upload structures under /inputs (PDB, CIF/MMCIF, PQR, SDF, MOL2, MMTF).
• Arguments are one flag per line. Folders are scanned recursively.
• Outputs go to /outputs/images and /outputs/animations. --output defaults to /outputs (normalized if overridden).

Important service behavior

• The service runs /ref/render.py and appends your args.
• Collage resolution and tile counts are capped for safety; use --allow-large-run to bypass.
• Static and angle modes emit PNGs; rotate/trajectory modes emit videos plus frame PNGs.

Arguments

• --input (required): file or directory of structures (.pdb, .ent, .pqr, .cif/.mmcif, .mmtf, .mol2, .sdf). Default: none (required).
• --output: base output dir; normalized to /outputs. Default: /outputs (service-normalized).
• --mode: static, angle, rotate, trajectory.
• --grid ROWSxCOLS: collage layout. Default: 1x1.
• --batch N: limit how many collages to produce; 0 means all.
• --order: sequential or random. Default: sequential.
• --rep: PyMOL representation. Default: spheres.
• --res: per-tile edge in pixels; capped 4096. Default: 512.
• --bgcolor: background color; none for transparent.
• --zoom_distance: optional camera zoom distance override.
• --start_angle: starting yaw (degrees).
• --angle_inc: degrees between frames for rotate. Default: 5.
• --fps: frames per second for animations. Default: 10.
• --reverse: reverse state/angle order. Default: false.
• --vid_format: mp4 or webm.
• --tmp-dir: scratch location for intermediate PNGs.
• --log-level: debug|info|warning|error|critical. Default: info (or RENDER_LOG_LEVEL).
• --pymol_settings ...: one or more tokens; key=value becomes set key, value, otherwise do <token> runs inside PyMOL. Default: none.
• --allow-large-run: bypass grid/res safety caps. Default: false.

Quick start

One PNG per structure, cartoon representation:

--input=/inputs/
--mode=static
--res=512
--rep=cartoon
--pymol_settings=do color marine, all
--bgcolor=black

Static collages

--input=/inputs/my_complex.pdb
--grid=2x2
--res=1024
--rep=surface
--pymol_settings=do util.cbc all
--bgcolor=black
--mode=static

Turntable animation

--input=/inputs/my_complex.pdb
--mode=rotate
--angle_inc=5
--fps=20
--vid_format=mp4
--rep=spheres
--pymol_settings=do color chainbow, byres all
--bgcolor=none

Angle collage (multi-view still)

--input=/inputs/my_complex.pdb
--mode=angle
--grid=2x3
--res=640
--rep=cartoon
--start_angle=0
--bgcolor=black

Animated collage (multiple inputs)

--input=/inputs
--mode=rotate
--grid=2x3
--res=640
--rep=cartoon
--bgcolor=black
--angle_inc=10
--fps=15
--vid_format=mp4
--order=random
--batch=4

Trajectory render

--input=/inputs/trajectory.pdb
--mode=trajectory
--fps=12
--vid_format=webm
--reverse
--bgcolor=none

Styling controls

Send PyMOL commands via --pymol_settings. Examples:

--input=/inputs/my_complex.pdb
--mode=static
--rep=sticks
--pymol_settings=do show cartoon, chain A
--pymol_settings=do util.cba chain B
--pymol_settings=do color tv_red, resi 45-60
--pymol_settings=set cartoon_side_chain_helper,1

Camera distance can be set with --zoom_distance=<value> (normally omit to use defaults).