- PYMOL TUTORIAL CHAIN HOW TO
- PYMOL TUTORIAL CHAIN MOVIE
- PYMOL TUTORIAL CHAIN INSTALL
- PYMOL TUTORIAL CHAIN DOWNLOAD
- PYMOL TUTORIAL CHAIN WINDOWS
Here you write which commands pymol should execute, and so it only take 1 second to get the same. The real power of PyMOL, comes into power, when your write a PyMOL command file.
PYMOL TUTORIAL CHAIN HOW TO
The box in the lower right corner will show how to move and rotate the molecule in this case. If you have a one or two button mouse you can change the mode in the Mouse menu in the Tcl/Tk GUI window. Try to move it around holding the middle button (moves the view) or the right button (zooms in and out). Try to move the mouse around while pressing the left mouse button. Ok, now we are going to try to move the molecule around. The cartoon option gives us the best overview of the overall structure, so hide the other representations and show the protein only in cartoon mode.Ĭolor everything white selecting C > grey > white. Try also to show the molecule as ribbon, sticks or surface to get a feeling for the different representations. Visualize the molecule in the cartoon representation by selecting S > cartoon. This will remove the line representation of the molecule. Press these buttons to see the options available in each menu. Later on we will make new selections that will appear in this menu.Įach of the two lines have 5 buttons labeled A (Actions), S (Show), H (Hide), L (Label), C (Color). In the right hand side of the viewer window there is a selection menu that currently contains two lines:Īll and the four character name of the PDB file, ex. The Viewer window should now contain the PDB file displayed with lines. Or we can write: fetch followed by the PDB id in either of the two command lines. We can then open the PDB file (if you have it on the harddisk) using the menu File > Open.
PYMOL TUTORIAL CHAIN DOWNLOAD
Protein structures are deposited at There are several ways to open this file:Įither we can download the file from PDB and save it to our computer. One can, however, get really far without ever having to worry about writing any commands.įirst, we will need to load a structure file into the program.
PYMOL TUTORIAL CHAIN WINDOWS
The upper window entitled PyMOL Tcl/Tk GUI controls the general settings and functionalities of the program while the lower one entitled PyMOL viewer,Ĭontains the settings that are related to the current display of the molecule.Įach of these two windows contain a command line, where we can enter commands into the program. When you open PyMOL you will see two windows opening. This tutorial does not cover all the functions of PyMol, but tries to focus on the most important ones.Ī great resource for more advanced use is this wiki and the large number of good tutorials found online, which can be accessed via google. This tutorial is designed to give you a basic working knowledge of making pretty and informative pictures of protein structures using PyMOL.
These homepages collect material from several sources, and present them in easy format. There exist homepages, to get more info about your protein. We need to find a Protein Databank File (PDB), which describe the x,y,z coordinates of your enzyme.įind a suitable file by searching for: porcine kidney fructose 1,6-bisphosphatase You don't have to follow the steps of extending PyMOL, but if you are a little technical, and want to become friends with PyMOL over time, then consider it. Consider this little nice texteditor: Notepad++
PYMOL TUTORIAL CHAIN INSTALL
If you want to read about PyMOL, then try this introduction Practical_Pymol_for_Beginners Install PyMOL to your computer We will only cover the very basic steps to get a image of your enzyme and put in your written student article. This is the very first introduction to the powerful molecular visualizer PyMOL. This tutorial was written directly for biochemistry students at Copenhagen University, 2012/2013.
PYMOL TUTORIAL CHAIN MOVIE
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