Create Methane Molecule in PyMol

This section provides a tutorial on how to create a methane molecule by exporting a single carbon atom and adding hydrogens in PyMol.

With selection and exporting functionalities, we can actually build a simple molecule like Methane in PyMol.

1. Export Carbon atom as a selection to an SDF file: Carbon-Atom.sdf:

delete all
reset
load Molecule-HY-001.sdf

hide all
show lines

select carbon, id 6
save Carbon-Atom.sdf, carbon, -1, sdf

2. Load Carbon-Atom.sdf and add hydrogens build the Methane molecule:

delete all
reset
load Carbon-Atom.sdf

h_add

3. Show Methane molecule in "sticks" representation:

hide all
show sticks

4. Export Methane molecule in an SDF file:

save Molecule-Methane.sdf, all, -1, sdf

Here you go! A methane molecule is created in an SDF file.

Create Methane Molecule in PyMol
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

 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