Model-to-Camera Space Coordinates Mapping

Molecule Tutorials - Herong's Tutorial Examples

∟Model-to-Camera Space Coordinates Mapping

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

In previous tutorials, we have learned how to use "turn" and "move", to change camera viewing angle and position, which impacts how the molecule structure is mapped from the model space to the camera space.

Below is the mapping formula used by PyMol.

Assuming:

we have the following mapping relation:

We can also write the mapping relation in the vector notation as:

or:

where M is the rotation matrix:

Now let's verify this mapping formula by looking the methane molecule.

1. Load the methane molecule structure to PyMol again. You see the structure displayed at the center of the screen, which is perpendicular to the z-axis of the camera space.

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

2. Get the view mapping parameters, which include the rotation matrix and the rotation center.

PyMOL>get_view
### cut below here and paste into script ###
set_view (\
  1.000000000,    0.000000000,    0.000000000,\ # M: rotation matrix
  0.000000000,    1.000000000,    0.000000000,\ # M: rotation matrix
  0.000000000,    0.000000000,    1.000000000,\ # M: rotation matrix
  0.000000000,    0.000000000,  -14.178204536,\ # D: camera rotation center
  0.840320110,   -1.029980063,   -0.000119984,\ # B: model rotation center
 11.178204536,   17.178203583,  -20.000000000 )
### cut above here and paste into script ###

3. Get coordinates of the carbon atom in the model space.

PyMOL>select carbon, id 5
 Selector: selection "carbon" defined with 1 atoms.
PyMOL>get_extent carbon
 cmd.extent: min: [   0.840,  -1.030,   0.000]
 cmd.extent: max: [   0.840,  -1.030,   0.000]

4. Run the formula on the carbon atom location. We get (0.000, 0.000, -14.178) in camera space. So the carbon atom should be displayed at the center of the screen.

5. Repeat the calculation on hydrogen atom #4.

PyMOL>select h4, id 4
 Selector: selection "h4" defined with 1 atoms.
PyMOL>get_extent h4
 cmd.extent: min: [   0.732,  -1.977,   0.529]
 cmd.extent: max: [   0.732,  -1.977,   0.529]