Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
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.
Table of Contents
Molecule Names and Identifications
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
Create Selection with Mouse in PyMol
Substructure Selection Visualization in PyMol
Modify Molecule Structure in PyMol
Export Molecule Substructure in PyMol
►Create Methane Molecule in PyMol
ChEMBL Database - European Molecular Biology Laboratory
PubChem Database - National Library of Medicine
INSDC (International Nucleotide Sequence Database Collaboration)
HGNC (HUGO Gene Nomenclature Committee)