Molecule Tutorials - Herong's Tutorial Examples

∟PyMol GUI and CLI

∟Virtual Trackball Rotation on PyMol

This section provides a quick introduction of Virtual Trackball Rotation model used by PyMol to rotate the molecule structure in 3-dimensions.

Once the molecule structure is displayed in the viewer window, you can rotate the molecule structure in 3-dimensions using the virtual trackball rotation model as described below.

1. The molecule structure is attached to a virtual trackball with the center of thr structure located at the center of the trackball.

2. The center of the trackball is fixed at the center of a 3-dimensional coordinate system on the screen with x-axis displayed horizontally, y-axis displayed vertically, and z-axis displayed perpendicular to the screen.

3. The trackball can be rotated by the left mouse button in 4 ways:

• Click the trackball at the center and drag is vertically to rotate it about the x-axis.
• Click the trackball at the center and drag is horizontally to rotate it about the y-axis.
• Click the trackball on the left or right edge and drag is vertically to rotate it about the z-axis.
• Click the trackball on the top or bottom edge and drag is horizontally to rotate it about the z-axis.

The following diagram (source: "Introduction to PyMOL" by DeLano Scientific LLC) shows you the virtual trackball rotation model used in PyMol:

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 DNA Sequencing

 Gene Mutation

 SDF (Structure Data File)

 PyMol Installation

►PyMol GUI and CLI

 PyMol Screen Layout

 Load Molecule from File into PyMol

►Virtual Trackball Rotation on PyMol

 Zoom In and Out on PyMol

 PyMol Command Line Interface

 "load" and "delete" Commands on PyMol

 "log_open" and "log_close" Commands on PyMol

 Model Space and Camera Space on PyMol

 "get_view" and "set_view" on PyMol

 View Parameters Auto Adjusted on PyMol

 Zoom In/Out by Moving Camera

 Rotation with Transformation Matrix

 Rotation with "turn" Command

 Difference of "turn" and "rotate" Commands

 Difference of "move" and "translate" Commands

 "center", "zoom" and "reset" Commands

 Model-to-Camera Space Coordinates Mapping

 Camera-to-Model Space Coordinates Mapping

 Turn Structure around Camera

 "show lines" Presentation Command

 "show sticks" Presentation Command

 "show spheres" Presentation Command

 "show surface" Presentation Command

 "show mesh" Presentation Command

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 HGNC (HUGO Gene Nomenclature Committee)

 Relocated Tutorials

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB

Virtual Trackball Rotation on PyMol - Updated in 2023, by Herong Yang