PyMol GUI and CLI

This chapter provides quick introductions about PyMol GUI (Graphical User Interface) and CLI (Command Line Interface).

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

Takeaways:

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 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