PyMol Editing Functions

This chapter provides quick introductions on using PyMol to edit molecule structure using 'edit' to identify picked atoms, and 'replace/attach' command to replace or attach new atoms to picked atoms in PyMol.

"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

Takeaways:

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

 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