Ceci est une ancienne révision du document !
Several pieces of specialised software exist to view and manipulate data. One such program is called PyMOL and is used by protein chemists and structural biologists around the world, to visualize the three-dimensional structures of the building blocks of life: proteins, RNA and DNA.
As the name indicates, PyMOL is a program written in python. Development was started in 2000 by Warren Lyford DeLano as an open source project. Compiled binaries were made available to paying customers who do not want the hassle of compiling the software themselves, obviously making it an advantage to use the software on GNU/Linux because a lot of nice people would compile PyMOL for the platform, so every day users can install it from the archives.
A special version “Incentive PyMOL” was also made available, containing special extra features that many users would not need, but would be a great addition to have for industrial partners and similar users.
Unfortunately, in late 2009, Warren DeLano passed away suddenly, and the future of the project was uncertain for a while, until Schrödinger Inc. took over the development and rights to PyMOL. Recently, a version 2.0 was released, with a compiled version of the open source code available for all major platforms. A license is still required to gain full access to all functions of the software.
For the current article, I will focus on a version that is a bit older, corresponding to what most GNU/Linux users will have in the archives of their favorite distribution.
sudo apt install pymol
should get PyMOL installed for you, and the program can be started either from the program launcher you use, or by typing pymol in a terminal.
Start it up and see what happens!
The PyMOL graphical user interface
PyMOL has two windows when opened: A window with an external graphical user interface (GUI), and a window with a viewer and an internal graphical user interface (GUI). The external GUI can be used to edit settings, to issue commands for making movies, and so on. This is also where the plugin system can be used. PyMOL can be extended through plugins, and several researchers around the world have made their code available for use with PyMOL.
The internal GUI and viewer area are used to visualize the molecules of interest and to manipulate representation of the molecules loaded into the program. The bottom right corner includes a quick overview of the functions of the mouse, which can be changed by clicking inside the box. At the bottom of the viewer, written commands can be used, the function of which is equal to the functions available by using the mouse.
If a list of PyMOL commands is written in a text file (a PyMOL–script), this can also be loaded when starting the program, enabling easy sharing of graphical views of molecules.
Getting the coordinates
Historically, most molecular coordinates have been experimentally determined by the x-ray crystallography technique. The Protein Data Bank (PDB) was established in 1971 and currently contains more than 123,456 structures of proteins, RNA and DNA. Currently, NMR, and, more recently, cryo–EM, are also used as techniques to determine the three-dimensional coordinates of macromolecular structures.
Coordinates are deposited by researchers from all over the world, and made available for everybody to investigate and gain insight into the microscopic world of some of the smallest parts of our cells.
In PyMOL, a plugin is already installed that can be used to load molecular coordinates – if the PDB-id is known. For this article, I will use 1mbo, which is one of the first protein structures that were determined by x-ray crystallography, the protein myoglobin.
To download the coordinates and load it into PyMOL, I will use the command-line command fetch
fetch 1mbo
which should result in the picture shown left (or something similar)
Here, the coordinates are loaded in the viewer and the internal GUI shows the object 1mbo is loaded.
In the internal GUI, the object can be hidden by pressing the name, and there are five buttons to the right of the object name: A - The action button, for different actions on the object S - The show button, to show different representations H - The hide button, to hide different representations L - The label button, to show labels on individual coordinates C - The color button, to color the coordinates
Now the structure is loaded into the viewer and we can make a representation of the protein.
Making a pretty picture
The structure of myoglobin we have loaded contains two interesting objects. A heme group, which is an organic compound that contains an iron-ion in the middle of the molecule, and an oxygen molecule, with the oxygen molecule being coordinated by the iron in the heme.
Several presets exist in the PyMOL interface, and we will use the mouse to choose the A button then preset, ligand site and finally cartoon.
This function can also be called from the command line with:
preset.ligand_cartoon(“1mbo”)
To get a good orientation of the interesting feature of the molecule, we will use the commands to zoom into the heme in the structure:
zoom resn HEM
Now use the mouse to rotate the view to your liking. You will notice that the lower right box indicates how you can interact with the viewer, and that the L, M and R indicate the mouse buttons. Press the left mouse button and move the mouse to rotate the molecule. You can also hold down the right mouse button to zoom in or out, and the middle mouse button to move the view.
To get a more clear view, you can hide the waters by using the H button next the the 1mbo object and press waters, to hide the representation of the waters in the molecule. You might also have noticed the yellow striped dots. These are water bonding interactions called polar contacts, and can be turned off by de-selecting the new object 1mbo_pol_conts (click on the name of the object and it is hidden). And finally we can show the oxygen as a sphere representation, to more clearly visualize them. We will first set the size of the spheres to be slightly smaller than usual.
set sphere_scale, 0.5 show spheres, resn OXY
Once you have found a nice view, you can use the ray command in the top right of the external GUI and then go to File –> Save Image As –> PNG and voilá, you have a picture of a molecule of oxygen bound to myoglobin from the Physeter catodon also known as the sperm whale.
I hope you enjoyed this very small introduction to the molecular viewer PyMOL