PyMOL, install Python Molecular Graphics on Ubuntu using Flatpak

about PyMOL

In the next article we are going to take a look at PyMol. Python Molecular Graphics is a program that will allow us to manipulate and visualize molecules, and that we can install in Ubuntu thanks to its Flatpak package. This is one of the few open source visualization tools available for use in structural biology.

As for the Py part of the name of this program, it refers to the fact that it is extensible thanks to the Python programming language. According to wich, can be extended to perform complex analysis of molecular structures using libraries available for Python, as they are NumPy or pylab.

PyMOL is an open source molecular viewer created by Warren Lyford Delano and marketed by Delano Scientific LLC, which is a company dedicated to creating universally accessible tools for the scientific and educational communities. This program is also suitable for producing high-quality 3D images of small molecules and biological macromolecules. PyMOL has the ability to load, manipulate, and visualize molecules from a variety of formats and sources.. The program can be easily controlled via a menu-based GUI or from a large number of keyboard shortcuts and / or scripts. A is available raytracer integrated to generate high quality images for the generated views.

examples of pymol

This is a commercial product, but most of its source code is available from its repository at GitHub free of charge under a permissive license. This project is maintained by Schrödinger and ultimately funded by everyone who acquires a PyMOL license.

General characteristics of PyMOL

PyMOL Adanaced settings

  • The program offers quality graphics. A built-in ray tracer brings shadows and depth to any scene. We can also render externally.
  • Create Videos can be as simple as loading multiple PDB files and press play.
  • Images can be copied and pasted directly into PowerPoint and Keynote. Still images and rendered sequences can be generated in PNG format and as QuickTime videos.
  • The arbitrary logical expressions make viewing and editing easy.
  • It has surface interpretations good, and mesh surfaces are also supported.
  • The cartoons with PyMOL they are easy to create and render.
  • The program will allow us control it from command line and from GUI.

PyMOL working

  • Structures can be cut, mutated and reassembled on the fly and write to standard files (PDB, MOL / SDF).
  • This application can be installed to view, analyze and prepare graphical images of proteins and experimental structural data (e.g. crystallographic, NMR-based and electron microscopy).
  • One of the best ways to control PyMOL is through reusable scripts, which can be written in command language or Python.
  • Cross-platform code. It has a single code base that is compatible with Unix, Macintosh and Windows, using OpenGL and Python, in addition to a small set of open source external dependencies.
  • The development of the user interface has focused primarily on capabilities, not ease of use for new users.
  • There are a single monolithic command-oriented programming interface.

These are just some of the features of this this program. They can consult all of them in detail from the Wiki of the project.

Install PyMOL on Ubuntu via Flatpak

This program can be found available at Flathub. For install Python Molecular Graphics on Ubuntu via Flatpak, it is necessary to have this technology enabled in our equipment. If you use Ubuntu 20.04 and do not have it, you can follow the guide that a colleague wrote in this blog about it.

When you can install this type of package on your computer, it is only necessary to open a terminal (Ctrl + Alt + T) and use the following command in it to install the program through Flatpak:

install with flatpak

flatpak install --user

In case you need update the program, when a new version is available, in a terminal it is only necessary to execute the command:

flatpak --user update org.pymol.PyMOL

After installation, we can start the program from the Applications menu or any other application launcher that we have available. We can also execute in the terminal (Ctrl + Alt + T) the command:

pymol launcher

flatpak run org.pymol.PyMOL


In case you want uninstall Python Molecular Graphics from your computer, you will only need to open a terminal (Ctrl + Alt + T) and execute in it:

uninstall PyMOL

flatpak uninstall org.pymol.PyMOL

PyMOL is a capable molecular viewer and renderer. It can be used to prepare publication-quality figures, to share interactive results, or to generate pre-rendered animations. Today, many scientists around regularly use PyMOL for these tasks. Users who want to know more about this program or how it works, can go to the Web page or to Wiki of the project.

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