Table of Contents

NOTE: This manual is ancient and obsolete!

Current PyMOL subscribers can access updated online documentation.

Non-subscribers can access The FREE PyMOL Community Wiki.

• Copyright Notice
• Terms of Usage for the PyMOL User's Manual
• Trademarks

• Why PyMOL?
• Words of Caution
• Strengths
• Weaknesses

• Welcome to PyMOL!
• Is PyMOL Free Software?
• Yes, but...
• The DeLano Scientific Mission

• Windows
• Recommendations
• Minimal System Requirements
• Python-Free Installation
• Python-Dependent Installation
• MacOS X
• Recommendations
• Minimial Requirements
• If you use Fink
• If you do not use Fink
• Linux and Unix
• System Requirements
• Dependency-Free Approaches
• Dependency-Based Approaches

• Launching
• Using the Mouse
• Using a Command Line
• PyMOL's Windows
• The Viewer Window
• The External GUI Window
• Loading PDB Files
• Manipulating the View
• Basic Mouse Control
• Virtual Trackball Rotation
• Moving Clipping Planes
• Changing the Origin of Rotation
• Getting Comfortable

• Recording Your Work (Optional)
• Loading Data
• Manipulating Objects
• Atom Selections
• Coloring Objects and Selections
• Turning Objects and Selections On and Off
• Changing Your Point of View
• Saving Your Work
• Scripts and Log Files
• png Files
• Session Files
• Command-Line Shortcuts
• Command Completion using TAB
• Filename Completion using TAB
• Automatic Inferences
• Other Typed Commands and Help

• Syntax
• Selection-expressions
• Named Atom Selections
• Single-word Selectors
• Property Selectors
• Selection Algebra
• Atom Selection Macros
• Calling Python from within PyMOL

• Background
• Accessibility
• Pretty and Correct
• Customization
• Cartoon Types
• Fancy Helices
• Secondary Structure Assignment

• Important Settings
• Saving Images
• png

• Introduction
• Supported Stereo Modes
• Crosseye Stereo
• Walleye Stereo
• Hardware Stereo
• Generating Stereo Figures

• Concepts
• States and Frames
• Important Commands To Know
• load
• mset
• mdo
• mmatrix
• Simple Examples
• Complex Examples
• Previewing Ray-traced Movie Images
• cache_frames
• mclear
• Saving movies
• mpng

• Picking Atoms and Bonds
• Example Usage of the "pk" Atom Selections
• The "lb" and "rb" Selections
• Conformational Editing

• Crystal Symmetry
• load
• symexp
• Electron Density Maps
• load
• isomesh and isodot

• Introduction
• Molscript Ribbons
• load
• Using Molscript
• Creating Compiled Graphics Objects
• CGO Reference
• load_cgo

• Introduction
• Example
• load_callback