pymol command not found

In this troubleshooting guide we learn how to fix pymol command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

pymol: command not found

or when using sudo you get the following error message

sudo: pymol: command not found

Solutions to pymol: command not found

How To Fix pymol: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu pymol is provided by pymol package.

pymol is:

PyMOL is a molecular graphics system targeted at medium to large biomolecules like proteins. It can generate high-quality publication-ready molecular graphics images and animations.

Features include:

  • Visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals
  • Molecular builder and sculptor
  • Internal raytracer and movie generator
  • Fully extensible and scriptable via a Python interface

File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps.

To fix this problem, we can install more using the command below.

sudo apt-get -y install pymol

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install pymol.

sudo apt -y install pymol

Or if you have aptitude installed you can use the following command.

sudo aptitude install pymol

Summary

In this tutorial we learn how to fix pymol command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.