pymol
TLDR
Launch PyMOL GUI
$ pymol
Open structure file$ pymol [structure.pdb]
Run script$ pymol [script.pml]
Command line mode$ pymol -c [script.pml]
Render image$ pymol -c -d "load [file.pdb]; ray; png [output.png]"
SYNOPSIS
pymol [options] [files...]
DESCRIPTION
PyMOL is a molecular visualization system for 3D structures of proteins, nucleic acids, and small molecules. It provides publication-quality graphics and extensive scripting capabilities.
PARAMETERS
-c
Command line only (no GUI).-d command
Execute command.-p
Read commands from stdin.-q
Quiet mode.-r script
Run Python script.-e
Exit after script.
EXAMPLES
$ # Launch and load structure
pymol protein.pdb
# Batch rendering
pymol -c -d "load 1abc.pdb; hide all; show cartoon; ray; png output.png; quit"
# Run script
pymol script.pml
# Fetch from PDB
pymol -d "fetch 1crn; show cartoon"
pymol protein.pdb
# Batch rendering
pymol -c -d "load 1abc.pdb; hide all; show cartoon; ray; png output.png; quit"
# Run script
pymol script.pml
# Fetch from PDB
pymol -d "fetch 1crn; show cartoon"
COMMANDS (PML)
$ load file.pdb # Load structure
fetch 1abc # Download from PDB
show cartoon # Display style
color red, chain A # Coloring
ray # Render
png output.png # Save image
fetch 1abc # Download from PDB
show cartoon # Display style
color red, chain A # Coloring
ray # Render
png output.png # Save image
CAVEATS
Open-source version has some limitations. Educational and commercial licenses available. Memory-intensive for large structures.
HISTORY
PyMOL was created by Warren DeLano starting in 1998, now maintained by Schrödinger, Inc. with open-source development.
