Molecule Tutorials - Herong's Tutorial Examples

∟PyMol GUI and CLI

∟Rotation with Transformation Matrix

This section provides a tutorial on how to rotate the molecule structure by changing the transformation matrix in the viewing parameters in PyMol.

We can also use the transformation matrix in the viewing parameters to rotate the molecule structure, if we follow the rule on how coordinate transformation matrix is applied.

For example, the following transformation matrix will rotate the molecule structure 90 degrees about the z-axis. 

  0.0, 1.0, 0.0
 -1.0, 0.0, 0.0
  0.0, 0.0, 1.0

If we put the above transformation matrix into the "set_view" command together with the camera zoom out location of (0.0, 0.0, -36.0), we will see the molecule got rotated and shrunken: 

PyMOL>set_view (\
     0.000000000,    1.000000000,    0.000000000,\
    -1.000000000,    0.000000000,    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

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 DNA Sequencing

 Gene Mutation

 SDF (Structure Data File)

 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)

 HGNC (HUGO Gene Nomenclature Committee)

 Relocated Tutorials

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB