PyMOL+

Workflow

• Upload structures under /inputs (PDB, CIF, 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.

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

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).