Connect with us

Software

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

Dr. Muniba Faiza

Published

on

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.

Preparing system

Let’s update and upgrade our system first.

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading prerequisites

First, you have to download MSMS. So, let’s change to the directory where we want to download the package. I am creating a new directory named ‘msms’ in the Downloads directory. Now download MSMS either by clicking here or using the following command.

$ cd Downloads/

$ mkdir msms

$ cd msms/

$ wget https://ccsb.scripps.edu/msms/download/933/

Downloading PyVOL

Now, let’s download the zip file of PyVOL from here or you can use the following command.

$ wget https://github.com/schlessinger-lab/pyvol/archive/refs/heads/master.zip

Installing MSMS

Let’s untar the package inside our new directory.

$ cd msms/

$ tar xvzf msms_i86_64Linux2_2.6.1.tar.gz

Now, create symbolic links to the binaries and add them to the path.

$ sudo ln -s /home/user/Downloads/msms/msms.x86_64Linux2.2.6.1 /usr/local/bin/msms

$ sudo ln -s /home/user/Downloads/msms/pdb_to_xyzr* /usr/local/bin

You have to debug two files before running msms.

  • Open the pdb_to_xyzr file in an editor and go to line 34:
    $ sudo nano /home/user/Downloads/msms/pdb_to_xyzr
    On line 34, you will see:
    numfile = "./atmtypenumbers"
    Change it to:
    numfile = "/home/user/Downloads/msms/atmtypenumbers"
  • Repeat the above steps for another file named pdb_to_xyzrn

Now, you can check the msms installation by typing $ msms in the terminal. It should display:

$msms
MSMS 2.6.1 started on structure
Copyright M.F. Sanner (1994)
Compilation flags -O2 -DVERBOSE -DTIMING
MSMS: No input stream specified

Installing PyVOL

  • Open Pymol –> Plugin –> Plugin Manager.
  • Install New Plugin –> Choose File.
  • Go to the directory where you downloaded the zip file of PyVOL (Downloads directory) and select it.
  • It will show “The plugin is installed”. Close the plugin Manager window.
  • Go to Plugin –> Select PyVOL.
  • Under the ‘Settings’ tab, you will see two columns. Under the right column, there is ‘Install PyVOL from PyPi’. Click on it. Wait for a few moments. It will install PyVOL and will display the packages installed additionally.
  • Further, under the MSMS settings, you will see the MSMS path.

References

  1. Smith, RH, Dar, AC, & Schlessinger, A. (2019). PyVOL: a PyMOL plugin for visualization, comparison, and volume calculation of drug-binding sites. BioRxiv , 816702.
  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

Docking

[Tutorial] Performing docking using DockingPie plugin in PyMOL.

Dr. Muniba Faiza

Published

on

[Tutorial] Performing docking using DockingPie plugin in PyMOL.

DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.

(more…)

Continue Reading

Docking

How to install the DockingPie plugin on PyMOL?

Dr. Muniba Faiza

Published

on

How to install DockingPie plugin on PyMOL?

DockingPie [1] is a plugin of PyMOL [2] made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).

(more…)

Continue Reading

Software

Video Tutorial: Calculating binding pocket volume using PyVol plugin.

Dr. Muniba Faiza

Published

on

Calculate Binding Pocket Volume in Pymol (using PyVol plugin).

This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].

(more…)

Continue Reading

Software

How to generate topology from SMILES for MD Simulation?

Dr. Muniba Faiza

Published

on

How to generate topology from SMILES for MD Simulation?

If you need to generate the topology of molecules using their SMILES, a simple Python script is available.

(more…)

Continue Reading

Software

[Tutorial] Installing jdock on Ubuntu (Linux).

Dr. Muniba Faiza

Published

on

[Tutorial] Installing jdock on Ubuntu (Linux).

jdock is an extended version of idock [1]. It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).

(more…)

Continue Reading

Software

How to upgrade cmake on Ubuntu (Linux)?

Dr. Muniba Faiza

Published

on

How to upgrade cmake on Ubuntu/Linux?

In bioinformatics, cmake is used to install multiple software including GROMACS, jdock, and so on. Here is a short tutorial on how to upgrade cmake on Ubuntu and get rid of the previous version. (more…)

Continue Reading

Software

How to install GMXPBSA on Ubuntu (Linux)?

Dr. Muniba Faiza

Published

on

How to install GMXPBSA on Ubuntu (Linux)?

GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA version 2.1.2 on Ubuntu (Linux).

(more…)

Continue Reading

Docking

[Tutorial] Installing Pyrx on Windows.

Dr. Muniba Faiza

Published

on

[Tutorial] Installing Pyrx on Windows.

Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows. (more…)

Continue Reading

MD Simulation

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Dr. Muniba Faiza

Published

on

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.

(more…)

Continue Reading

Software

Installing Autodock4 on MacOS.

Dr. Muniba Faiza

Published

on

Installing Autodock4 on MacOS

Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.

(more…)

Continue Reading

Docking

How to install Autodock4 on Ubuntu?

Dr. Muniba Faiza

Published

on

How to install Autodock4 on Ubuntu?

Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.

(more…)

Continue Reading

Software

DS Visualizer: Uses & Applications

Dr. Muniba Faiza

Published

on

DS Visualizer: Uses & Applications

Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins [1]. Here are some uses and applications of DS Visualizer.

(more…)

Continue Reading

Software

Protein structure & folding information exploited from remote homologs.

Dr. Muniba Faiza

Published

on

protein structure & folding prediction using remote homologs

Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)

Continue Reading

RNA-seq analysis

Pathonoia- A new tool to detect pathogens in RNA-seq data.

Dr. Muniba Faiza

Published

on

Pathonoia- A new tool to detect pathogens in RNA-seq data.

Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].

(more…)

Continue Reading

Software

AlphaFill- New algorithm to fill ligands in AlphaFold models.

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

Software

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

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

Software

How to generate electron density map using Pymol?

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

Software

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

Dr. Muniba Faiza

Published

on

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.

(more…)

Continue Reading

Software

How to install Kpax on Ubuntu (Linux)?

Published

on

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…)

Continue Reading

Secondary structure

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

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

LATEST ISSUE

ADVERT