Molecule Tutorials - Herong's Tutorial Examples

Copyright © 2019-2019 Dr. Herong Yang. All rights reserved.

Molecule This book is a collection of notes and tutorial examples written by the author while he was learning molecules and related tools. Topics include understanding atoms, bonds and molecules; molecule SDF (Structure Data File) format; generating PNG pictures from molecule SDF files; visualizing molecule structure in 3-D with PyMol; generating molecule movie with PyMol. Updated in 2019 (Version 1.01): added SDF tutorials.

Table of Contents

About This Book

Introduction of Molecules

What Is Molecule

What Is Molecular Formula

What Is Atomic Bond

What Is Molecule Structure

SDF (Structure Data File)

What Is SDF (Structure Data File)

SDF Format Specification

Convert SDF to SVG

PyMol Installation

What Is PyMol

Install PyMol Incentive Edition on macOS

Install PyMol Open Source Edition

Compile PyMol Source Code

Install Open Source PyMol with Homedrew

Install Open Source PyMol with Fink

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

Create Selection with Mouse in PyMol

"select" Command in PyMol

Substructure Selection Visualization in PyMol

Modify Molecule Structure in PyMol

Export Molecule Substructure in PyMol

Create Methane Molecule in PyMol

PyMol Editing Functions

"pk1", "pk2", "pk3" and "pk4" Selections

"edit id n1, id n2, id n3, id n4" Commands

"remove pk*" and "remove_picked" Commands

"unbond pk1, pk2" and "bond pk1, pk2" Commands

"replace new_atom, ..." Replace pk1 with New Atom

"attach new_atom, ..." Attach to pk1 with New Atom

Build Alcohol Molecule with PyMol

PyMol Measurement Functions

"get_extent" - Picked Atom Location

"label" - Generate Labels on Atoms

Distance between Atoms in PyMol

Angle Formed by 3 Atoms in PyMol

Dihedral Angle Formed by 3 Atoms in PyMol

Use Selection Expressions in PyMol

"get_area" - Surface Areas of Atoms

Surface Area of Bonded Atoms

Surface Area of Entire Molecule

"get_position" - Viewing Center

PyMol Movie Functions

What Is State in PyMol

Frames and "mset" Command

"mplay" Command and Movie Settings

mdo" Command to Change Views

"madd/minsert/mdelete/mcopy/mmove" Commands

"until.mroll()" - Movie Rolling Function

"movie.produce" - Export Movie File in MPEG Format

PyMol Python Integration

Run Python Statements from PyMol

PyMol Python API

Launch PyMol from Python Interpreter

PyMol Python API Only Functions

PyMol Object Functions

What Is Object in PyMol

Visualize Objects Independently

Edit Objects Independently


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Keywords: Molecule, PyMol, SDF