Create Selection with Mouse in PyMol

This section provides a tutorial on how to create a new selection by selecting atoms with mouse in a molecule in PyMol.

You can use PyMol to visualize a molecule structure as a whole. Or you can define sub-sets of the molecule as selections and manage visualization of each selection independently.

The first step to create a selection is to select atoms from the molecule to be included in the selection.

The simplest way to select atoms is click their locations on the screen and name the selection.

1. Load the molecule from the SDF file, Molecule-HY-001.sdf. You see the molecule in the default representation.

2. Change the representation to "lines" with two commands:

hide all
show lines

3. Click on "Selecting" mode to change it to "Atoms". The "Selecting" mode is located in the mouse control area near the bottom right corner of the viewer window.

4. Click on all 6 C atoms on the benzene ring in the lower part of the molecule. You see selected atoms identified with small pink squares. You also see a new entry called "(sele)" displayed on the right side of the viewer window.

5. Click "A" on the "(sele)" entry to open the action menu. And click "rename selection" from the menu. You see a rename message on the viewer window.

6. Enter "ring" as the name of the object created with those selected atoms. You can also rename the "sele" to "ring" with the "set_name sele, ring" command.

Now we have create a new selection called "ring" representing a sub-set of the molecule.

Create Selection in PyMol
Create Selection 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