Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
Zoom In/Out by Moving Camera
This section provides a tutorial on how to zoom in and zoom out on the molecule structure by changing the camera location (origin of camera rotation) in PyMol.
If we understand the PyMol viewing parameter correctly, we should be able to zoom in and zoom out on molecule structure by changing the camera location (origin of camera rotation).
After loading the molecule from Molecule-HY-001.sdf, we know that the origin of camera rotation (location of the camera) is automatically adjusted to (0.0, 0.0, -17.18). So if we move it half way towards the screen at (0.0, 0.0, -8.0), the molecule will probably enlarged about twice of the original size to get the zoom in result.
With the camera moved, we also need to move the slabs (clipping planes in the camera direction) to 0.0 and 1000.0 respectively to ensure that the molecule is located between the slabs.
Run the following "set_view" command with changed viewing parameters described above. You should see the molecule enlarged, the zoom in result.
set_view (\ 1.000000000, 0.000000000, 0.000000000,\ 0.000000000, 1.000000000, 0.000000000,\ 0.000000000, 0.000000000, 1.000000000,\ 0.000000000, 0.000000000, -8.000000000,\ 0.876923084, -0.289230824, 0.000000000,\ 0.000000000, 1000.000000000, -20.000000000 )
If you want to zoom out on the displayed structure, you can move the camera location away from the screen by changing the origin of camera rotation to (0.0, 0.0, -36.0), run the following "set_view" command:
PyMOL>set_view (\ 1.000000000, 0.000000000, 0.000000000,\ 0.000000000, 1.000000000, 0.000000000,\ 0.000000000, 0.000000000, 1.000000000,\ 0.000000000, 0.000000000, -36.000000000,\ 0.876923084, -0.289230824, 0.000000000,\ 0.000000000, 1000.000000000, -20.000000000 )
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)