Molecule Tutorials - Herong's Tutorial Examples - v1.26, by 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 viewing 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
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)
HGNC (HUGO Gene Nomenclature Committee)