"log_open" and "log_close" Commands on PyMol

This section provides a tutorial on how to open an log file to record all PyMol commands and re-run them on PyMol.

You can use "log_open" and "log_close" commands to open a log file to record all commands you entered through the PyMol interface.

You can re-run all commands in a log file by entering the log file with the "@*" command.

Here is what I did to open a log file, record some commands, and run the log file:

1. Open a new log file in the home directory:

PyMOL>log_open /Users/herong/pymol.log

2. Delete all objects and reset viewin parameters:

PyMOL>delete all
PyMOL>reset

3. Load a molecule structure from the a SDF file:

PyMOL>load /Users/herong/Molecule-HY-001.sdf

CmdLoad: loaded as "Molecule-HY-001".

4. Rotate the molecule -45 degrees about the z-axis:

PyMOL>rotate z, 45

5. Close the log file:

PyMOL>log_close

6. Run the log file. You see the molecule loaded and rotated.

PyMOL>@/Users/herong/pymol.log

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