Table of Contents
Description
PyMOL: A molecular visualization system that can produce high-quality 3D images of small molecules and biological macromolecules.
Schrödinger, LLC
Website/Download
Publisher and License Information
Schrödinger, LLC – Open Source
Input & Output
| Input | Output |
|---|---|
| – Molecular Structures – Trajectories & Topologies – Volumetric Data – Geometry – Scripts – Annotated Structures | – Molecular Structures – Volumetric Data – Geometry – Images |
File Types
| Category | Extension |
|---|---|
| Molecular Structures | PDB, mmCIF, CIF, MOL2, MOL, SDF, PKL, MAE, MOE, PQR |
| Trajectories & Topologies | TOP, Amber TRJ, Gromacs TRJ, TRR, XTC, GRO, G96, DCD |
| Volumetric Data | CCP4, XPLOR, OMAP, PHI, DX, Cube, MTZ |
| Geometry | Raster3D, VRML2, POV, COLLADA |
| Scripts & Annotated Structures | PML, P1M, P5M, Python |
Screenshots
Courtesy of Schrödinger, LLC.
Documentation
Topics
Welcome | Installation | Loading Molecules | Mouse Controls | Rendering | Movies | Core Commands | Labels | Enhancements | Unsupported Features | 3D Stereographic Viewing | Molecular Morphing (RigiMOL) | Volume Visualization
Reference
Concepts | Settings | Selections | Commands | A.P.I. | Launching | Python | Java | File Formats | Representations | SEURAT | Platforms | Performance | Using AxPyMOL
Narrated Screencasts
Examples
Figures | Animations | Scripting
Troubleshooting
General | Windows | Macintosh | Performance | Stability | Linux | Virtual Machines
Links
PyMOLWiki | Google | pymol.org | schrodinger.com
Legal Notices
Schrödinger EULA | List of PyMOL Third-Party Software, Libraries and Utilities