Build Alcohol Molecule with PyMol

This section provides a tutorial on how to build an alcohol molecule with PyMol commands.

PyMol also have a command add hydrogen atoms to the molecule structure if there are not include with the "h_add" command.

Together with "h_add" and "replace" commands, we have build an alcohol molecule from a single carbon atom.

delete all
reset

# load the carbon atom from an SDF file
load Carbon-Atom.sdf
hide all

# add hydrogen atoms to form the methane molecule
h_add
show sticks

# replace one hydrogen atom to carbon
edit id 2
replace C, 1, 1

# replace another hydrogon atom to oxygen
edit id 3
replace O, 1, 1

# save the molecule to an SDF file
save Alcohol-Molecule.sdf, all, -1, sdf

The result is an alcohol molecule. Some hydrogen atoms are not located in correct angles. I can fix them later.

Build Alcohol Molecule in PyMol
Build Alcohol 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