PyMol Measurement Functions

Molecule Tutorials - Herong's Tutorial Examples

∟PyMol Measurement Functions

This chapter provides quick introductions on using PyMol to access measurements and properties of substructures or the entire molecule in PyMol.

"get_extent" - Picked Atom Location

"label" - Generate Labels on Atoms

Distance between Atoms in PyMol

Angle Formed by 3 Atoms in PyMol

Dihedral Angle Formed by 3 Atoms in PyMol

Use Selection Expressions in PyMol

"get_area" - Surface Areas of Atoms

Surface Area of Bonded Atoms

Surface Area of Entire Molecule

"get_position" - Viewing Center

Takeaways:

PyMol "get_extent" command prints the extent of a selection in the console window. If the selection is a single atom, the extent becomes a point representing the location of the atom.
PyMol "label" command generates a label on the specified atom using Python string format patterns with atom properties as variables.
PyMol "get_distance" command prints the distance of 2 picked atoms.
PyMol "distance" command generates a label to show the distance of 2 picked atoms.
PyMol "get_angle" command prints the angle formed by 3 picked atoms.
PyMol "distance" command generates a label to show the angle formed by 3 picked atoms.
PyMol "get_dihedral" command prints the dihedral angle formed by 4 picked atoms.
PyMol "dihedral" command generates a label to show the dihedral angle formed by 4 picked atoms.
PyMol "get_area" command prints the surface area of a selection.
PyMol "get_position" command prints the viewing center location in the model space.