"select" Command in PyMol

This section provides a tutorial on how to create a new selection by using the 'select' command an selection expression in PyMol.

You can create selections in PyMol by clicking atom locations. But you can also create selections by the "select" command:

select selection_name, selection_expression

"selection_expression" - An set of preperty name and value-list pairs joined by Boolean operators to identify a group of atoms in a molecule.

For example, the following command create a new selection named as "group_1" with all C or N atoms and indexed as 1, 2, or 3 in the molecule structure.

select group_1, name C+N and id 1+2+3

Let's create the "ring" selection again with the "select" command:

PyMOL>log_open Selection-Create-Ring.pml
PyMOL>delete all
PyMOL>reset
PyMOL>load Molecule-HY-001.sdf
 CmdLoad: loaded as "Molecule-HY-001".
PyMOL>hide all
PyMOL>show lines

PyMOL>select ring, id 6+9+10+11+12+13
 Selector: selection "ring" defined with 6 atoms.

Now we have create the same selection "ring" as the previous tutorial with the "select" command without using the mouse.

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