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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.

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

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