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« Back to Software Grid. PyMOL is licensed to MIT for educational and academic research use by MIT faculty, staff, and students. Download (MIT certificate required) PyMOL license key for all systems Mac. Free Download: BIOVIA Discovery Studio Visualizer Molecular visualization is a key aspect of the analysis and communication of modeling studies. If you need a commercial-grade graphics visualization tool for viewing, sharing, and analyzing protein and modeling data, complete the form below to receive the free Discovery Studio Visualizer for. Pymol, Free Download by Schrodinger. Log in / Sign up. Mac › Design & Photo › 3D Modeling › Pymol › Download. PyMOL is a powerful and comprehensive molecular visualization product. Download Review Comments Questions & Answers. PyMOL A free and open-source molecular graphics system for visualization, animation, editing, and publication-quality imagery. PyMOL is scriptable and can be extended using the Python language. Supports Windows, Mac OSX, Unix, and Linux.

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• 2Install PyMOL to your computer
• 3Find a suitable protein data file
• 6The 'Faster' way
• 7Movie of Epidermal Growth Factor
• 9Export movies

Biochemistry course

This tutorial was written directly for biochemistry students at Copenhagen University, 2012/2013.

This is the very first introduction to the powerful molecular visualizer PyMOL.
We will only cover the very basic steps to get a image of your enzyme and put in your written student article.

If you want to read about PyMOL, then try this introduction Practical_Pymol_for_Beginners

Install PyMOL to your computer

You first want to install PyMOL.
Do this, by following this guide.

Windows

Windows Pre-compiled_PyMOL. Consider this little nice texteditor: Notepad++

mac

pymol for mac. Download and install MacPyMOL-v1.3r1-edu.tar.bz2

Extending pymol

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.

Find a suitable protein data file

We need to find a Protein Databank File (PDB), which describe the x,y,z coordinates of your enzyme.
These are stored at the homepage: http://www.rcsb.org
Find a suitable file by searching for: porcine kidney fructose 1,6-bisphosphatase
The PDB file 1LEV, seems suitable.

Read more about your protein

There exist homepages, to get more info about your protein.
These homepages collect material from several sources, and present them in easy format.

http://www.proteopedia.org/wiki/index.php/1lev
http://pdbwiki.org/wiki/1lev

Background

This tutorial is designed to give you a basic working knowledge of making pretty and informative pictures of protein structures using PyMOL.
This tutorial does not cover all the functions of PyMol, but tries to focus on the most important ones.
A great resource for more advanced use is this wiki and the large number of good tutorials found online, which can be accessed via google.

When you open PyMOL you will see two windows opening.
The upper window entitled PyMOL Tcl/Tk GUI controls the general settings and functionalities of the program while the lower one entitled PyMOL viewer,contains the settings that are related to the current display of the molecule.
Each of these two windows contain a command line, where we can enter commands into the program.
One can, however, get really far without ever having to worry about writing any commands.

First, we will need to load a structure file into the program. Protein structures are deposited at www.pdb.org
There are several ways to open this file:
Either we can download the file from PDB and save it to our computer.
We can then open the PDB file (if you have it on the harddisk) using the menu File > Open.
or we can write: fetch followed by the PDB id in either of the two command lines. Ex: fetch 1LEV
The Viewer window should now contain the PDB file displayed with lines.

In the right hand side of the viewer window there is a selection menu that currently contains two lines:
all and the four character name of the PDB file, ex. 1lev.
Later on we will make new selections that will appear in this menu.
Each of the two lines have 5 buttons labeled A (Actions), S (Show), H (Hide), L (Label), C (Color).
Press these buttons to see the options available in each menu.

Hide the line representation. Press H > everything in the all line. This will remove the line representation of the molecule.
Visualize the molecule in the cartoon representation by selecting S > cartoon.
Try also to show the molecule as ribbon, sticks or surface to get a feeling for the different representations.
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.
Color everything white selecting C > grey > white.

Ok, now we are going to try to move the molecule around.
Try to move the mouse around while pressing the left mouse button. This will rotate the molecule.
Try to move it around holding the middle button (moves the view) or the right button (zooms in and out).
If you have a one or two button mouse you can change the mode in the Mouse menu in the Tcl/Tk GUI window.
The box in the lower right corner will show how to move and rotate the molecule in this case.

Start your PyMOL

Start your shortcut to PyMOL 'C:Python27PyMOLPyMOL.exe'

Now click and do the following:

1. Write in command line: fetch 1lev
2. Right Menu: -> 1lev -> 'A' -> preset -> Publication
3. Top Menu: Display -> Sequence
4. Top Menu: Display -> Sequence Mode -> Chains
5. In Sequence, select so all 'F' is marked.
6. Right Menu: -> (sele) -> 'A' -> remove atoms. (1LEV is crystallized in dimer formation. So we only need to view 1 chain)
7. Top Menu: Display -> Sequence Mode -> Residue Codes
8. In Sequence, select so only substrate (F6P) is marked (A/338)
9. Right Menu: -> (sele) -> 'A' -> zoom
10. Right Menu: -> (sele) -> 'A' -> rename selection -> f6p
11. Right Menu: -> (f6p) -> 'C' -> by element -> Select to Carbon is not green
12. Right Menu: -> (f6p) -> 'A' -> find polar contacts -> to others excluding solvent
13. In Sequence, select so only MN is marked (A/340)
14. Right Menu: -> (sele) -> 'A' -> rename selection -> mn
15. Right Menu: -> (mn) -> 'S' -> spheres
16. Write in console: select act_site, byres f6p around 3.5
17. Right Menu: -> (act_site) -> 'S' -> sticks
18. Right Menu: -> (act_site) -> 'L' -> residues
19. Top Menu: Display -> Background -> White
20. Find a good view, and push 'Ray' in the top right of the grey command console.
21. Top Menu: File -> Save Image As -> PNG
22. Put it into your student article

The 'Faster' way

The real power of PyMOL, comes into power, when your write a PyMOL command file.
Here you write which commands pymol should execute, and so it only take 1 second to get the same.
The commands are stored in a '.pml' file.

Open Notepad, and then: File->Save as->All files-> C:UsersYOUpymol1lev.pml

1. '#' Line starting with hashes is not read by PyMOL. Use a comment field.
2. Best to restart PyMOL every time from fresh
3. Go to your working directory
4. Get the pdb file from the RCSB server. async=0 makes sure it waits for completion of download before continuing.

Then you just open the .pml file with PyMOL.
Or start PyMOL, and write in command: @1lev.pml
Or start PyMOL, top menu -> File -> Run... -> C:UsersYOUpymol1lev.pml

Movie of 1LEV

File: 1lev_movie.pml
Note, you need the movie.pml file in same directory, see Biochemistry_student_intro#By_a_movie_file.

Movie of Epidermal Growth Factor

Lets make a movie of the Molecule of the month on RCSB.org.
Let's take a membrane protein, 1nql@rcsb, pdbwiki, proteopedia
June 2010 Molecule of the Month by David Goodsell

Open Notepad, and then: File->Save as->All files-> C:UsersYOUpymol1nql.pml

GUI - Scene loop

1. Click Movie->Program->Scene Loop->Steady->Program->4 seconds each
2. Click the Play button at the lover right corner. Or write mplay.
3. Click Movie->Reset
4. Try also the other Scene Loop method.

GUI - Camera loop

1. Click Mouse-># Button Motions. In the selection menu, under all, you now have a M button!.
2. Movie->Reset
3. Click F1
   1. sel. menu all-[M]->Store with scene F1
   2. Movie->Program->Camera Loop->Y-Roll->4 seconds
   3. Movie->Append->2 seconds
   4. Click lower right Full forward button->
4. Click F2
   1. sel. menu all-[M]->Store with scene F2
   2. Movie->Program->Camera Loop->X-Rock->60. deg. over 4 sec.
   3. Movie->Append->2 seconds
   4. Click lower right Full forward button->
5. Click F3
   1. sel. menu all-[M]->Store with scene F3
   2. Movie->Program->Camera Loop->X-Roll->4 seconds
   3. Movie->Append->2 seconds
   4. Click lower right Full forward button
6. Click F4
   1. sel. menu all-[M]->Store with scene F4
   2. Movie->Append->1 seconds
   3. Click lower right Full forward button
   4. sel. menu all-[M]->Store with scene F4
   5. Movie->Program->Camera Loop->Nutate->30. deg. over 8 sec.
   6. Movie->Append->4 seconds
   7. Click lower right Full backward button

Play

By a movie file

Open Notepad, and then: File->Save as->All files-> C:UsersYOUpymolmovie.pml

Write in pymol: @movie.pml

Movie of Potassium Channel KcsA-Fab complex in high concentration of K+

Let's take another membrane protein, 1k4c@rcsb, pdbwiki, proteopedia

Open Notepad, and then: File->Save as->All files-> C:UsersYOUpymol1k4c.pml

Export movies

Pymol Download Free Version

Write in command

Then go to File->Save Movie As -> MPEG
It takes a little time, 5 min. Be patient.

You can also export it like PNG images, and then collect them.
Then go to File->Save Movie As -> PNG Images

If you wan't to have a really nice movie, you want to have all images ray-traced. Then do

But note, this takes a looong time, so wait until you are SURE that you have the final movie. Try first to make and collect a video without.

Collect images and create movie in 'Windows Live Movie Maker'

Start or install Windows Live Movie Maker

1. Add all images from folder
2. Ctrl+a to select all images
3. Click in tab 'Edit', set Duration to: 0,03
4. Click in tab 'Home', 'Save movie', 'Windows Phone (large)'

You are done

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