Molecular modeling and structural visualization using PyMOL, an open-source molecular visualization tool. The goal was to analyze and represent the structure of the Histone protein (PDB: 6KIX) and develop a movie highlighting key structural elements and interactions in a clear, educational format.
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Software: PyMOL Molecular Graphics System
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Input: Protein Data Bank File –
6KIX.pdb -
Scripting: PyMOL commands and session management
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Movie Creation: Scene setting, rendering, and frame transitions
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File Formats:
.pml,.pse,.mp4 -
Load and visualize the Histone protein structure from the Protein Data Bank.
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Create custom selections of secondary structure components:
- Alpha helices
- Beta sheets
- DNA strands
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Generate and render a PyMOL movie with multiple scenes, each representing a specific biological insight.
The generated movie includes the following scenes:
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Alpha Helices
Visualize only the alpha helices of the Histone protein. -
Alpha Helices with Polar Contacts & Hydrogen Bonds
Adjusted transparency to show backbone and highlight hydrogen bonds. -
Beta Sheets with Polar Contacts
Focused orientation and polar interactions highlighted. -
DNA Double Helix
DNA strands extracted and emphasized. -
Full Molecule – Publication Mode
Enhanced visuals using publication-style rendering. -
DNA Wrapped Around Histone Core
The full protein-DNA complex, showcasing the DNA wrapping mechanism.
- Extra attention was paid to polar interactions, visual clarity, and aesthetic transitions between scenes.
- Custom colors and transparency settings were applied for educational emphasis.
- Movie rendering was optimized for smooth transitions and clear molecular presentation.
You can find the generated movie and snapshots in the media/ folder .
This project is licensed under the MIT License.
You are free to use, modify, and distribute this project for educational and research purposes, but proper credit must be given to the original author (Noora-Alhajeri).
© 2025 Noora-Alhajeri. All rights reserved.
Originally Developed: Novermber 27, 2021
Uploaded to GitHub: 2025
For questions or collaboration, feel free to reach out:
📧 Email: n.s3eedalhajeri@gmail.com
🌐 LinkedIn: Noora-Alhajeri