Molecule Tutorials - Herong's Tutorial Examples - v1.21, by Dr. 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.
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