Molecule Tutorials - Herong's Tutorial Examples - v1.21, by Dr. Herong Yang
"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
Molecule Names and Identifications
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
RDKit: Open-Source Cheminformatics Software
Load Molecule from File into PyMol
Virtual Trackball Rotation on PyMol
"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
Rotation with Transformation Matrix
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
"show lines" Presentation Command
"show sticks" Presentation Command
"show spheres" Presentation Command
"show surface" Presentation Command
"show mesh" Presentation Command
ChEMBL Database - European Molecular Biology Laboratory
PubChem Database - National Library of Medicine
INSDC (International Nucleotide Sequence Database Collaboration)