Substructure Selection Visualization in PyMol

This section provides a tutorial on how to visualize a substructure selected from a molecule differently than the entire molecule structure in PyMol.

Once a selection is created, you visualize it differently than the whole molecule by specifying the selection name in the "show" command:

show representation_name, selection_name

Let's create the "ring" selection again by running all commands recorded in the log file.

PyMOL>@Selection-Create-Ring.pml
...

PyMOL>hide all

PyMOL># show the molecule in "lines" representation
PyMOL>show lines

PyMOL># show the selection in "sticks" representation
PyMOL>show sticks, ring

Now the molecule structure is visualized with 2 representations superposed over each other.

Substructure Selection Visualization in PyMol
Substructure Selection Visualization in PyMol

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

 Create Selection with Mouse in PyMol

 "select" Command in PyMol

Substructure Selection Visualization in PyMol

 Modify Molecule Structure in PyMol

 Export Molecule Substructure in PyMol

 Create Methane Molecule in PyMol

 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

 References

 Full Version in PDF/EPUB