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How to run LigAlign plugin on Pymol?

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How to run LigAlign plugin on Pymol?

Running a plugin on an old version of Pymol [1] can give you multiple errors that are not easy to troubleshoot. For example, LigAlign plugin [2] runs on an old version of Pymol. Previously, we explained how to install LigAlign on Pymol. In this article, we will run the LigAlign command on Pymol.

After a successful installation of the LigAlign plugin, you will see “LigAlign v1.00 loaded” on the Pymol console. But when you try to run this plugin, it still gives you errors including,

“ExecutiveLoad-Error: Unable to open file ‘2bxa'” OR

“NameError: global name ‘CmdException’ is not defined”

Therefore, you will have to perform some additional steps to make it run. They are explained below.

Preparing input

Let’s take three PDB structures as input. You can use any complex structure. We are using 2BXA, 2BXB, and 2BXC.

  • Download these structures in any format, PDB or CIF. We are using the CIF format here.
  • Copy these downloaded structures in the same directory where the ligand_alignment.py script is located. This script is present inside the ligalign directory. If you haven’t installed ligalign yet, then visit this link.

Running LigAlign

  • Open Pymol. Change to the directory where the ligand_alignment.py script is located. For example,
    PYMOL> cd /home/user/Downloads/ligalign
    It will display the path on the console.
  • Now open those structures. Go to File –> Open –> Select the structures.
  • Run the following command in the Pymol console.
    PYMOL> ligalign 2bxa.cif, 2bxb.cif, 2bxc.cif
  • You will see aligned ligands in the display and RMS values in the console.

If this doesn’t work then follow the steps shown below:

  • Open Pymol. Change to the directory where the ligand_alignment.py script is located. For example,
    PYMOL> cd /home/user/Downloads/ligalign
    It will display the path on the console.
  • Now fetch the structures.
    PYMOL> fetch 2bxa
    PYMOL> fetch 2bxb
    PYMOL> fetch 2bxc
  • Run the following command in the Pymol console.
    PYMOL> ligalign 2bxa.pdb, 2bxb.pdb, 2bxc.pdb
  • You will see aligned ligands in the display and RMS values in the console.

References

  1. Heifets, A., & Lilien, R. H. (2010). LigAlign: flexible ligand-based active site alignment and analysis. Journal of Molecular Graphics and Modelling29(1), 93-101.
  2. 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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AlphaFill- New algorithm to fill ligands in AlphaFold models.

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AlphaFill- New algorithm to fill ligands in AlphaFold models.

AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)

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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.

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