Molecule Tutorials - Herong's Tutorial Examples

∟PyMol GUI and CLI

∟Camera-to-Model Space Coordinates Mapping

This section provides a tutorial on how to map camera space coordinates to model space coodinates manually using the reverse of the rotation matrix in PyMol.

In the last tutorial, we have used the following mapping relation to map a point in model space to camera space:

where:

But what about mapping a point in the camera space to the model space? It is also easy to do, if you know how to reverse the rotation matrix, using the "numpy" Python module.

1. Load the methane molecule structure to PyMol again. And convert viewing parameters into 'numpy' matrix and vectors: 

PyMOL>delete all
PyMOL>load Molecule-Methane.sdf
 CmdLoad: loaded as "Molecule-Methane".

PyMOL>view = cmd.get_view()
PyMOL>M1 = [view[i] for i in range(0,3)]
PyMOL>M2 = [view[i] for i in range(3,6)]
PyMOL>M3 = [view[i] for i in range(6,9)]

PyMOL>M = numpy.matrix([M1, M2, M3])
PyMOL>D = numpy.matrix([[view[9]],[view[10]],[view[11]]])
PyMOL>B = numpy.matrix([[view[12]],[view[13]],[view[14]]])

2. Get the reverse of the rotation matrix and call it R: 

PyMOL>R = M.I

3. We are ready to convert any point in the model space, A, to the camera space, C:

where:

You can verify this with some examples.

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