PyMol Screen Layout

Molecule Tutorials - Herong's Tutorial Examples

∟PyMol GUI and CLI

∟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. Initially, the object area is empty.

4. Mouse information 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

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)

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

Full Version in PDF/EPUB