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

 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 Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

PyMol Object Functions

What Is Object in PyMol

 Visualize Objects Independently

 Edit Objects Independently

 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

 References

 Full Version in PDF/EPUB