Molecule Tutorials - Herong's Tutorial Examples

∟PyMol GUI and CLI

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

This section provides a quick introduction on 'center', 'zoom', and 'reset' commands to quickly adjust viewing parameters on PyMol.

PyMol also provides some commands to quickly adjust viewing parameters without changing molecule atom locations in model space.

"center" Command - Adjusts viewing parameters so that the molecule structure is displayed at the center of the screen.

"center" command is useful, in case the molecule structure has been rotated and/moved out of the display screen and you want to bring it back to the center.

"zoom" Command - Adjusts viewing parameters so that the molecule structure is displayed at the center of the screen and scaled to fit entirely inside the screen.

"zoom" command perform same functions as the "center" command, but it performs one more step to scale the molecule structure view to fit inside the screen.

"reset" Command - Adjusts viewing parameters so that the molecule structure is displayed at the center of the screen, scaled to fit entirely inside the screen, and restored to the default viewing direction.

"reset" command works like the "zoom" command, but it perform one more step to restore the default viewing direction (rotation transformation matrix is restored to the identity matrix).

Note that "center". "zoom" and "reset" commands only changes viewing parameters. They do not change molecule atom locations in the model space.

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