Download PyMOL User's Guide

Table of Contents
Copyright Notice and Usage Terms..................................................................................................................1
Copyright Notice......................................................................................................................................1
Terms of Usage for the PyMOL User's Manual......................................................................................1
Trademarks..............................................................................................................................................1
Preface..................................................................................................................................................................2
Why PyMOL?..........................................................................................................................................2
Words of Caution.....................................................................................................................................2
Strengths..................................................................................................................................................3
Weaknesses..............................................................................................................................................3
Introduction.........................................................................................................................................................4
Welcome to PyMOL!...............................................................................................................................4
Is PyMOL Free Software?.......................................................................................................................4
Yes, but..............................................................................................................................................4
The DeLano Scientific Mission...............................................................................................................4
Installation...........................................................................................................................................................6
Windows..................................................................................................................................................6
Recommendations.............................................................................................................................6
Minimal System Requirements.........................................................................................................6
Python−Free Installation...................................................................................................................6
Python−Dependent Installation.........................................................................................................6
MacOS X.................................................................................................................................................6
Recommendations.............................................................................................................................7
Minimial Requirements.....................................................................................................................7
If you use Fink...................................................................................................................................7
If you do not use Fink........................................................................................................................7
Linux and Unix........................................................................................................................................8
System Requirements........................................................................................................................8
Dependency−Free Approaches.........................................................................................................8
Dependency−Based Approaches.......................................................................................................9
Getting Started with Mouse Controls.............................................................................................................10
Launching..............................................................................................................................................10
Using the Mouse..............................................................................................................................10
Using a Command Line...................................................................................................................10
PyMOL's Windows................................................................................................................................11
The Viewer Window.......................................................................................................................11
The External GUI Window.............................................................................................................12
Loading PDB Files.................................................................................................................................13
Manipulating the View..........................................................................................................................13
Basic Mouse Control.......................................................................................................................13
Virtual Trackball Rotation...............................................................................................................14
Moving Clipping Planes..................................................................................................................16
Changing the Origin of Rotation.....................................................................................................16
Getting Comfortable........................................................................................................................17
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