Official Resources
- Homepage: https://pymol.org/
- Documentation: https://pymolwiki.org/index.php/Main_Page
- Source Repository: https://github.com/schrodinger/pymol-open-source
- License: Open-source (Open source build) / Commercial (Incentive PyMOL)
Overview
PyMOL is a molecular visualization system on an open-source foundation, maintained by Schrödinger. It is renowned for its high-quality rendering of biomolecules (proteins, nucleic acids) and its powerful Python scripting capabilities. PyMOL excels at creating publication-quality images and movies, and performing structural analysis like superposition and measurement.
Scientific domain: Molecular visualization, structural biology, rendering
Target user community: Structural biologists, biochemists, computational chemists
Theoretical Methods
- Ray tracing (built-in ray tracer)
- Molecular surface generation (solvent accessible surface)
- Electrostatic potential mapping (APBS plugin)
- Structural alignment (superposition algorithms)
- Molecular editing (mutagenesis, torsion adjustment)
Capabilities (CRITICAL)
- High-Quality Rendering: Ray-tracing for publication figures (shadows, occlusion)
- Representation: Cartoon, ribbons, sticks, spheres, surfaces, mesh, dots
- Analysis: RMSD alignment, hydrogen bond detection, distance measurement
- Scripting: Full Python API (
pymol module) and command language (pml scripts)
- Session Saving: Save state as
.pse files
- Plugins: Extensive ecosystem (e.g., APBS for electrostatics, Autodock for docking)
Sources: PyMOL Wiki, Schrödinger website
Inputs & Outputs
- Input formats: PDB, mmCIF, SDF, MOL2, XYZ, CCP4 map, XPLOR map, cube, DX
- Output data types: PNG/Ray-traced images, MPEG movies, PDB files, session files (.pse)
Interfaces & Ecosystem
- Python: Deep integration (PyMOL IS a Python interpreter extended with C libraries)
- Jupyter: Can be run within Jupyter notebooks (via ipymol or similar)
- APBS: Integration for electrostatics
- VMD: Complementary tool (VMD often for dynamics, PyMOL for static high-quality images)
Workflow and Usage
- Load structure:
load protein.pdb
- Style:
hide everything, show cartoon, show sticks, resn LIG
- Color:
color red, chain A, color blue, chain B
- Ray trace:
ray 2000, 2000
- Save image:
png image.png
Performance Characteristics
- Highly optimized rendering engine
- Can handle large protein complexes
- Open-source build may lack some performance features of the commercial Incentive PyMOL
Application Areas
- Structural biology (crystallography, Cryo-EM)
- Drug design (docking visualization)
- Molecular dynamics snapshots
- Educational illustrations
Community and Support
- PyMOLWiki (community maintained)
- PyMOL-users mailing list
- Open source and commercial versions
Verification & Sources
Primary sources:
- Homepage: https://pymol.org/
- Wiki: https://pymolwiki.org/
- GitHub: https://github.com/schrodinger/pymol-open-source
Confidence: VERIFIED
Verification status: ✅ VERIFIED
- Website: ACTIVE
- Documentation: COMPREHENSIVE (Wiki)
- Source: OPEN (GitHub)
- Development: ACTIVE (Schrödinger)
- Applications: High-quality rendering, structural biology, Python scripting