Export Molecule Substructure in PyMol

This section provides a tutorial on how to export a substructure identified as a selection in a molecule from PyMol.

Once a substructure is identified as a selection in PyMol, you can export the substructure to an SDF (Structure Data File) file.

1. Load the molecule from an SDF file: Molecule-HY-001.sdf:

PyMOL>delete all
PyMOL>reset

PyMOL>load Molecule-HY-001.sdf

2. Create the "ring" selection:

PyMOL>select ring, id 6+9+10+11+12+13
 Selector: selection "ring" defined with 6 atoms.

3. Click "File > Export Molecule" from the menu. You see a dialog box.

4. Select "ring" from the "Selection" list. And click "Save" button. You see another dialog box.

5. Select "MDL SD (*.sdf *.mol)" from the format list. And enter "Benzene-Ring.sdf" as the file name.

6. Click "Save" button. The "ring" substructure is saved an SDF file called "Benzene-Ring.sdf".

Export Subsctructure from PyMol
Export Subsctructure from 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