Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
View Parameters Auto Adjusted on PyMol
This section provides a tutorial to demonstrate how PyMol automatically calculate viewing parameters to ensure that the molecule structure is displayed in the center and enclosed entirely inside the viewing window.
When you load a molecule structure into PyMol, it will automatically adjust viewing parameters, so that the molecule structure will be displayed in the center of the screen and enclosed entirely inside the viewing window.
Here are atom locations of the molecule specified in the Molecule-HY-001.sdf file:
0.8400 -0.1600 0.0000 N 0 0 0 0 0 0 0 0 1.4800 0.4300 0.0000 N 0 0 0 0 0 0 0 0 0.0900 0.2700 0.0000 N 0 0 0 0 0 0 0 0 1.1100 1.2100 0.0000 C 0 0 0 0 0 0 0 0 0.2700 1.1200 0.0000 C 0 0 0 0 0 0 0 0 0.8400 -1.0300 0.0000 C 0 0 0 0 0 0 0 0 1.5300 1.9900 0.0000 C 0 0 0 0 0 0 0 0 1.0700 2.7400 0.0000 Cl 0 0 0 0 0 0 0 0 1.5900 -1.4600 0.0000 C 0 0 0 0 0 0 0 0 0.0800 -1.4600 0.0000 C 0 0 0 0 0 0 0 0 1.5900 -2.3300 0.0000 C 0 0 0 0 0 0 0 0 0.0700 -2.3200 0.0000 C 0 0 0 0 0 0 0 0 0.8400 -2.7600 0.0000 C 0 0 0 0 0 0 0 0
If I load the molecule into PyMol, the viewing parameters will be adjusted as shown below
PyMOL>load /Users/herong/Molecule-HY-001.sdf PyMOL>get_view ### cut below here and paste into script ### set_view (\ 1.000000000, 0.000000000, 0.000000000,\ 0.000000000, 1.000000000, 0.000000000,\ 0.000000000, 0.000000000, 1.000000000,\ 0.000000000, 0.000000000, -17.179622650,\ 0.876923084, -0.289230824, 0.000000000,\ 13.544545174, 20.814699173, -20.000000000 ) ### cut above here and paste into script ###
The output tells us that:
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)