Software
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
- Smith, RH, Dar, AC, & Schlessinger, A. (2019). PyVOL: a PyMOL plugin for visualization, comparison, and volume calculation of drug-binding sites. BioRxiv , 816702.
- The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.
Docking
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.
Software
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.
Software
Protein structure & folding information exploited from 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…)
RNA-seq analysis
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].
Software
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…)
Software
How to calculate binding pocket volume using PyVol plugin in PyMol?
Software
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.
Software
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.
Software
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…)
Secondary structure
How to run do_dssp command (mkdssp) 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…)
Software
Installing SMINA on Ubuntu (Linux).

SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy minimization [1]. In this article, we are going to install SMINA on Ubuntu (Linux). (more…)
Software
How to install ClusCo on Ubuntu (Linux)?

ClusCo is a bioinformatics software to perform clustering and comparison of protein models [1]. In this article, we are going to install ClusCo on Ubuntu (Linux). (more…)
Software
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. (more…)
Software
How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?

Few errors appear when we try to run the LigAlign plugin [1] in Pymol [2]. For example, if you try to run the ligand_alignment plugin, it will give you multiple errors including “Unable to initialize LigAlign v1.00“, or “can’t run LigAlign v1.00” or “incorrect Python syntax” or “Plugin has been installed but initialization failed“. In this article, we explain the reason for this issue and how you can rectify these errors. (more…)
Software
How to install multiple Pymol versions on Ubuntu (Linux)?

Sometimes we need to access old versions of Pymol [1]. Running some plugins on Pymol is difficult due to Python incompatibility. New Pymol versions require Python 3.x whereas older versions run on Python 2.x. Therefore, we need to maintain multiple versions of Pymol on a single system. In this article, we will install Pymol 1.7.x along with the latest version (Pymol 2.5.2) on Ubuntu. Later, we will create shortcuts for them.
Software
[Tutorial] Installing Pymol on Mac OS.

Previously, we provided a tutorial for Pymol installation on Ubuntu. In this article, we are going to install Pymol on Mac OS. (more…)
Software
How to install VMD on Ubuntu?

In this article, we are going to install VMD [1] on Ubuntu. (more…)
MD Simulation
How to install GROMACS on Apple M1 (MacOS)?

We have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS [1] on Mac OS. (more…)
Software
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. (more…)
MD Simulation
How to take snapshots of structure at specific times in GROMACS?

It is important to see the behavior of protein during an MD simulation. This can be achieved by taking snapshots in the form of PDB format. In this article, we have provided a few commands that you can use to take snapshots of a complete system or protein during MD simulation. (more…)
You must be logged in to post a comment Login