PyMol Screen Layout

This section provides a quick introduction of the PyMol screen layout.

Once PyMol is started, you should see two windows displayed:

External GUI - A Graphical User Interface window with the following areas:

1. Output message area - An area where output messages are displayed. Initially, the output area displays the following message:

Copyright (C) Schrodinger, LLC

This Executable Build integrates and extends Open-Source PyMOL.
Detected OpenGL version 2.1. Shaders available.
Detected GLSL version 1.20.
OpenGL graphics engine:
 GL_VENDOR:   ATI Technologies Inc.
 GL_RENDERER: AMD Radeon Pro 450 OpenGL Engine
 GL_VERSION:  2.1 ATI-1.51.8
No License File - For Evaluation Only (23 days remaining)
Detected 8 CPU cores.  Enabled multithreaded rendering.

2. Command input area - An area below the output message area where PyMol commands can be entered.

3. Command button area - An area on the right side of the output message area where a set of command buttons are displayed.

Viewer Window - A graphical display window with the following areas:

1. Viewer area - An area where the molecule is rendered as a graphical image. Initially, the molecule viewer displays a blank area.

2. Command input area - An area below the viewer area where PyMol commands can be entered.

3. Object name area - An area where a list of objects identified in the molecule is displayed. Initinaly, the object area is empty.

4. Mouse infomation area - An area where help information are displayed to tell you how to control the visualization with the mouse.

5. Movie control area - An area where movie editing and playing controls are displayed.

PyMol Screen Layout
PyMol Screen Layout

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