Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
What Is Object in PyMol
This section provides a quick introduction on the object concept used by PyMol to represent a unit of molecule structures.
What Is Object in PyMol? - An object is a concept used in PyMol to represent a unit of molecule structures loaded from a file.
A object is usually created by the "load" command:
load file_name [, object_name [, state_id ]]
"object_name" specifies the name of the object to which the molecule structure from the file will be loaded with the following use cases:
"state_id" specifies the state where the molecule structure will be loaded with the following use cases:
There are 2 PyMol settings controls how states are displayed:
Here are some examples of how molecule structures are loaded into objects in different states:
PyMOL>delete all PyMOL>count_state cmd.count_states: 0 states. PyMOL>load Molecule-Methane.sdf, Methane, 1 CmdLoad: loaded as "Methane". PyMOL>count_state cmd.count_states: 1 states. PyMOL>load Benzene-Ring.sdf, Ring, 2 CmdLoad: loaded as "Ring". PyMOL>count_state cmd.count_states: 2 states. PyMOL># load alcohol molecule into the default state 1 PyMOL>load Molecule-Alcohol.sdf, Alcohol CmdLoad: loaded as "Alcohol". PyMOL>count_state cmd.count_states: 2 states.
Now we have 3 objects in 2 states in the PyMol session.
Table of Contents
Molecule Names and Identifications
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
Visualize Objects Independently
ChEMBL Database - European Molecular Biology Laboratory
PubChem Database - National Library of Medicine
INSDC (International Nucleotide Sequence Database Collaboration)
HGNC (HUGO Gene Nomenclature Committee)