Model Space and Camera Space on PyMol

This section provides a quick introduction of model space and camera space cooridinate systems used on PyMol to transform and display molecule structures on the screen.

PyMol uses two coordinate systems to form the viewing model when the molecule structure is displayed on the screen.

1. Model Space Coordinate System - A 3-dimensional coordinate system in which molecule atom locations are specified.

For example, the following line in a SDF molecule file specifies a Carbon atom located at (1.1100, 1.2100, 0.0000) in the Model Space coordinate system.

    1.1100    1.2100    0.0000 C   0  0     0  0  0  0  0  0

2. Camera Space Coordinate System - A 3-dimensional coordinate system in the display screen and the viewing camera are specified:

When you reguest the molecule structure to be displayed on the screen, PyMol will perform a set of transformation to map the molecule structure from the model space to the camera space. This set of transformations is generated from viewing parameters you sepecified by viewing commands like "rotate", "move", etc.

The following diagram (source: "A Beginner’s Guide to Molecular Visualization Using PyMOL" By Nicholas Fitzkee) shows you the relation of the model space and the camera space used in PyMol:

Model Space and Camera Space on PyMol
Model Space and Camera Space on PyMol

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 SDF (Structure Data File)

 RDKit: Open-Source Cheminformatics Software

 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)

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB