Modify Molecule Structure in PyMol

This section provides a tutorial on how to modify a molecule structure by rotating and translating a substructure selected from the molecule in PyMol.

Selections in PyMol can be used to visualize substructures differently than the other parts of the molecule. Selections can also be used to modify molecule structure by specifying the selection name in the "rotate" and "translate" commands:

rotate x|y|z degree, selection_name
translate [vector], selection_name

Let's continue with the previous tutorial and modify the substructure defined by the "ring" selection.

PyMOL>@Selection-Create-Ring.pml
...

PyMOL># show the selection in "sticks" representation
PyMOL>show sticks, ring

PyMOL># modify substructure "ring"
PyMOL>rotate y, 30, ring
PyMOL>translate [1,0,0], ring

The molecule structure is modified now as shown on the screen.

Modify Molecule Structure in PyMol
Modify Molecule Structure 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