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Protein Visualization

How to find disulfides in protein structure using Pymol?

Tariq Abdullah

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find disulfides in protein structure using pymol

As shown in previous articles, Pymol [1] has several functions. In this article, we will show how to look for disulfide in protein crystal structures using Pymol.

Follow these steps:

  1. Open Pymol by typing pymol in a terminal in Ubuntu and in Windows, by double-clicking the shortcut or by searching.
  2. Go to File --> Open. Select a PDB structure to analyze.
  3. Set the color of the structure and background as you wish.
  4. Go to the right panel, click on the “S” column, it will show many functions.
  5. Select disulfides --> sticks. You can select any representation as you want. Other options include lines and spheres.
  6. If there are any disulfides present in the structure, it will display on the screen.

Make sure you haven’t made sticks/lines/spheres hidden from the “all” row in the top right panel.


Reference

  1. The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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