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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

Software

How to execute matlab from terminal in Ubuntu (Linux)?

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How to execute matlab from terminal in Ubuntu (Linux)?

While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.

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Software

How to install Kpax on Ubuntu (Linux)?

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How to install Kpax on Ubuntu (Linux)?

Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)

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Secondary structure

How to run do_dssp command (mkdssp) in Gromacs 2022?

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How to run do_dssp command in Gromacs 2022?

In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)

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