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

This section provides a tutorial on how to unbond or bond atoms from a molecule in PyMol using picked atoms as special selections, pk1, pk2, pk3 and pk4.

You can unbond or bond atoms picked atoms as pk1, pk2, pk3 and pk4 selections from the molecule structure. For example:

PyMOL># remove the bond between first two picked atoms:
PyMOL>unbond pk1, pk2

PyMOL># add a bond between first two picked atoms
PyMOL>bond pk1, pk2
MyMol Unbond and Bond Picked Atoms
MyMol Unbond and Bond Picked Atoms

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