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PyMol: Uses & Applications

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PyMol: Uses & Applications

PyMol is one of the most widely used bioinformatics software. Generally, it is used as a molecular viewer to visualize macromolecules and small molecules. In this article, we are discussing several uses and applications of PyMol.

  • To visualize different kinds of molecules such as proteins, compounds, or molecules.
  • You can also use it as a molecular builder. For more details, read this article.
  • To export files into different formats.
  • You can save sessions. For example, if you are working with a protein and would like to save a particular pose, then you can save it as a session and continue from that point later.
  • Measure bond lengths and find polar contacts between receptor and ligand.
  • Find disulfide bridges in a protein structure. For more details, read this article.
  • Save high-quality images in PNG format.
  • Export into different formats such as PDB.
  • Open different file formats such as sdf, pdb, pdbqt, and so on.
  • Perform various operations on structures such as removing atoms or residues, changing colors, labeling residues, and so on.
  • Easy install of plugins.

References

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

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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How to calculate binding pocket volume using PyVol plugin in PyMol?

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How to calculate binding pocket volume using PyVol plugin in PyMol?

Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol [2]. (more…)

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How to generate electron density map using Pymol?

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How to generate electron density map using Pymol?

Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.

(more…)

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Installing PyVOL plugin in Pymol on Ubuntu (Linux).

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Installing PyVOL plugin in Pymol on Ubuntu (Linux).

PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)

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