issue129:tutoriel1
Différences
Ci-dessous, les différences entre deux révisions de la page.
Prochaine révision | Révision précédente | ||
issue129:tutoriel1 [2018/01/27 12:45] – créée auntiee | issue129:tutoriel1 [2018/01/30 18:26] (Version actuelle) – andre_domenech | ||
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- | 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. | + | **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. | + | 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 " | + | Plusieurs logiciels spécialisés existent pour voir et manipuler des données. L'un d'eux s' |
- | Unfortunately, | + | Comme son nom l' |
- | 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. | + | **A special version " |
+ | |||
+ | Unfortunately, | ||
+ | |||
+ | Une version spéciale, appelée « Incentive PyMOL » (PyMOL incitatif) a été rendue disponible, contenant des fonctionnalités spéciales supplémentaires dont beaucoup d' | ||
+ | |||
+ | Malheureusement, | ||
+ | |||
+ | **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 | sudo apt install pymol | ||
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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. | 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! | + | Start it up and see what happens!** |
+ | |||
+ | Pour cet article, je me concentrerai sur une version qui est un peu plus ancienne, correspondant à ce que la plupart des utilisateurs sous GNU/Linux trouveront dans les archives de leur distribution préférée. | ||
+ | |||
+ | sudo apt install pymol | ||
+ | |||
+ | devrait installer pymol ; le programme peut démarrer, soit avec le lanceur de programme que vous utilisez, soit en tapant pymol dans un terminal. | ||
+ | |||
+ | Démarrez-le et regardez ce qui se passe ! | ||
- | The PyMOL graphical user interface | + | **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. | 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. | ||
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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. | 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), | + | If a list of PyMOL commands is written in a text file (a PyMOL–script), |
- | Getting the coordinates | + | L' |
+ | |||
+ | À l' | ||
+ | |||
+ | Le GUI interne et le visualiseur sont utilisés pour voir les molécules qui vous intéressent et pour manipuler les représentations des molécules chargées dans le programme. Dans l' | ||
+ | |||
+ | Si une liste de commandes est écrite dans un fichier texte (PyMOL-script - script PyMOL), elle peut être chargée au démarrage du programme, rendant facile le partage de vues graphiques des molécules. | ||
+ | |||
+ | **Getting the coordinates | ||
Historically, | Historically, | ||
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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. | 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, | + | 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, |
- | To download the coordinates and load it into PyMOL, I will use the command-line command fetch | + | Obtenir des coordonnées |
+ | |||
+ | Historiquement, | ||
+ | |||
+ | Les coordonnées sont déposées par des chercheurs du monde entier et sont disponibles à tous ceux qui cherchent à avoir une meilleure compréhension du monde microscopique de certaines des plus petites parties de nos cellules. | ||
+ | |||
+ | Dans PyMOL, un module est déjà installé qui peut être utilisé pour charger des coordonnées moléculaires, | ||
+ | |||
+ | **To download the coordinates and load it into PyMOL, I will use the command-line command fetch | ||
fetch 1mbo | fetch 1mbo | ||
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C - The color button, to color the 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. | + | Now the structure is loaded into the viewer and we can make a representation of the protein.** |
- | Making a pretty picture | + | Pour télécharger les coordonnées, |
+ | |||
+ | fetch 1mbo | ||
+ | |||
+ | dont le résultat est l' | ||
+ | |||
+ | Ici, les coordonnées sont chargées dans le visualiseur et le GUI interne montre que l' | ||
+ | |||
+ | Dans le GUI interne, l' | ||
+ | A - Le bouton d' | ||
+ | S - Le bouton de visualisation, | ||
+ | H - Le bouton de masquage, pour masquer les différentes représentations. | ||
+ | L - Le bouton d' | ||
+ | C - Le bouton de coloration, pour colorer les coordonnées. | ||
+ | |||
+ | Maintenant que la structure est chargée dans le visualiseur, | ||
+ | |||
+ | **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. | 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. | ||
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This function can also be called from the command line with: | This function can also be called from the command line with: | ||
+ | |||
+ | preset.ligand_cartoon(" | ||
+ | |||
+ | Créer une belle image | ||
+ | |||
+ | La structure de la myoglobine que nous avons chargée contient deux objets intéressants. Un groupe heme, qui est un composé organique qui contient un ion fer au milieu de la molécule et une molécule d' | ||
+ | |||
+ | Plusieurs préréglages existent dans l' | ||
+ | |||
+ | Cette fonction peut aussi être appelée en ligne de commande : | ||
preset.ligand_cartoon(" | preset.ligand_cartoon(" | ||
- | 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: | + | **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 | 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. | + | 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, | + | Pour obtenir une bonne orientation de la caractéristique intéressante de la molécule, nous utiliserons les commandes pour zoomer au sein du heme de la structure : |
+ | |||
+ | zoom resn HEM | ||
+ | |||
+ | Maintenant, utilisez la souris pour tourner la vue comme vous le préférez. Vous noterez que le champ le plus bas à droite indique comment vous pouvez interagir avec le visualiseur, | ||
+ | |||
+ | **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, | ||
set sphere_scale, | set sphere_scale, | ||
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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. | 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 | + | I hope you enjoyed this very small introduction to the molecular viewer PyMOL ** |
+ | |||
+ | Pour obtenir une vue plus claire, vous pouvez masquer les « waters » en utilisant le bouton H à côté de l' | ||
+ | |||
+ | set sphere_scale, | ||
+ | show spheres, resn OXY | ||
+ | |||
+ | Une fois que vous avez obtenu une jolie vue, vous pouvez utiliser la commande ray en haut à droite du GUI externe, puis aller à File (Fichier) -> Save image as (enregistrer l' | ||
+ | |||
+ | J' |
issue129/tutoriel1.1517053526.txt.gz · Dernière modification : 2018/01/27 12:45 de auntiee