"pk1", "pk2", "pk3" and "pk4" Selections

This section provides a quick intrdocution on speical selections, pk1, pk2, pk3 and pk4, used for molecule editing functions in PyMol.

PyMol supports 4 special selections called picked atoms named as, pk1, pk2, pk3 and pk4, that are used by molecule editing functions.

The easiest way to create "pk1", "pk2", "pk3" and "pk4" selections is to use the mouse click in "Editing" mode.

1. Load the molecule from Molecule-HY-001.sdf.

PyMOL>delete all
PyMOL>reset
PyMOL>load Molecule-HY-001.sdf

2. Click "Mouse Mode" to set it to "3-Button Editing" in the mouse control area near the bottom right corner of the viewer window.

3. Click an atom on the molecule. You see pk1 selection created for the selected atom.

4. Click 3 more atoms. You see all 4 special selections, pk1, pk2, pk3 and pk4, created and identified with different markers.

You can remove any pk* selection by click it again.

See next tutorials on how to use those 4 picked atoms (pk* selections).

MyMol Editing Selections: pk1, pk2, pk3, pk4
Create Methane Molecule 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

PyMol Editing Functions

"pk1", "pk2", "pk3" and "pk4" Selections

 "edit id n1, id n2, id n3, id n4" Commands

 "remove pk*" and "remove_picked" Commands

 "unbond pk1, pk2" and "bond pk1, pk2" Commands

 "replace new_atom, ..." Replace pk1 with New Atom

 "attach new_atom, ..." Attach to pk1 with New Atom

 Build Alcohol Molecule with PyMol

 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