Biochemistry student intro

Biochemistry course

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

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 windows computer

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

Start your PyMOL

Start your shortcut to PyMOL "C:\Python27\PyMOL\PyMOL.exe"

Now click and do the following:

1. Top Menu: Plugin -> PDB Loader Service -> 1lev OK
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
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. Find a good view, and push "Ray" in the top right of the grey command console.
20. Top Menu: File -> Save Image As -> PNG
21. 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:\Users\YOU\pymol\1lev.pml

# Best to restart PyMOL every time from fresh
reinitialize
cd C:\Users\DIG\pymol

fetch 1lev, async=0
preset.publication(selection='all')
remove chain F
select substrates, organic
select f6p, id 4770-4785
zoom f6p
util.cbac('f6p')

select act_site, byres f6p around 3.5
distance pol_cont, f6p, act_site, mode=2

select cli, /1lev//A/CLI
select mn, name MN
show spheres, mn

show sticks, act_site
label act_site and name CB, resn+resi

zoom pol_cont
viewport 1024,768
ray
png 1lev.png

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:\Users\YOU\pymol\1lev.pml