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
- 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.
Table of Contents
About This Book
Introduction of Molecules
Molecule Names and Identifications
Protein and Amino Acid
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
Gene and Chromosome
Protein Kinase (PK)
SDF (Structure Data File)
RDKit: Open-Source Cheminformatics Software
PyMol GUI and CLI
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)
Resources and Tools
Molecule Related Terminologies
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