Bioinformatics
Using Pymol for Protein Visualization
Pymol is an open source program for displaying and manipulating macromolecular structures. You
can use it at home. It can be found at: http://www.pymol.org. It may be easier to find the free version
by searching in Google on “Pymol download free”. You can download a windows version here:
http://download.cnet.com/3001-2054_4-10914845.html?spi=0441e5329155c352ee2f2ebe383acd32
How to start Pymol: Pymol is started when you double-click on a file from the Protein Data
Bank. These files are also free: you can download them from the internet. We will look at 1IGT.
Visualizing a Protein:
1. Go to the Protein Data Bank:
http://www.rcsb.org/pdb/home/home.do
2. In the textbox next to the search button at the top of the page type in:
Click the search button.
1IGT
3. This brings you to the page for the protein whose PDB ID is 1IGT.
At the top right-hand corner click on “Download Files”
Pull down to: “PDB File (Text)”
This causes the .pdb file to be downloaded to your computer.
4. Double-click on the file 1IGT.pdb. This starts Pymol, and 1IGT shows as “line
representation” in the bottom window, the Pymol Viewer. Viewing the protein in
different representations helps in understanding its structure. The top window is the
Pymol Molecular Graphics System window with a menu at the top and a place to enter
command at the “Pymol>” prompt.
5. With your mouse click and drag on an edge of the protein, so that you turn 1IGT to see
another side of it. Play around with it until you can turn it in all 3 spatial dimensions.
Zoom in on the protein. There are 2 ways to zoom in: one way uses your mouse. See if
you can find it. See if you can pick out a tyrosine residue. Here is what it looks like in
line, stick and sphere representations:
Looking at Different Representations of a Protein:
1. In the top right corner you see “1IGT” with buttons “A”, “S”, “H”, “L”, “C”. The button
“S” is what controls the way the protein is shown, while “H” controls what you hide.
Select show cartoon. Now select show “As” cartoon. What is the difference? Select Show
As spheres for space filling mode.
2. Can you make the representations additive? Show 1IGT with cartoon representation
overlaid on stick representation overlaid on line representation.
3. Use the button “H”=hide to subtract the sticks and the lines so only cartoon is left. With
cartoon representation you can see secondary structure: alpha helices, beta sheets and
loops. You can also see the different chains. Use the button “C” = color and select “color
by chain”. There are a few different ways to do this. Pick one that you like for printing.
Here are images of secondary structure: a helix, a loop and a sheet.
Saving and printing an image:
1. At the top of the Pymol Molecular Graphics System window see the menu choices. For
printing choose Display … Background … White. Display … Color Space … CMYK is
for printing, while RGB looks better on your screen.
2. Do a ray trace in preparation for printing. At the bottom of the Pymol Molecular Graphics
System window is the command line. Type in “ray, 1200, 1200” and wait for the ray
trace to complete. Do not click on the image until you’ve saved it. Notice that a box has
appeared containing a high quality mage of the protein.
3. From the file menu on this same window choose “Save image as” … PNG. Save it to a
location where you can find it for printing.
Chains, Residues and Atoms:
1. Next to 1IGT select the button L=Label. Label the chains. Color by chain also to help you
see the structures. Rotate the protein to look at it from different angles. At the bottom
right of the Pymol Viewer there is a down arrow between buttons S and F. Click this
button so that Pymol will turn the protein for you so you can see it better. You can toggle
“full screen” mode on and off with the F button.
2. At the command line type “center chain A” and zoom in. See how a chain is an unbroken
structure. Chain A intertwines with chain B.
3. Type “center chain B” and notice that chain B is longer than chain A and intertwines with
both chain A and chain D.
4. Press the S button to show the residue in the protein in fasta format. Each chain has its
residues numbered from 1. The chains are in order: A, B, C, D.
5. Select all of chain A by dragging your mouse along all the residues of chain A (use the
slider to get access to them all). The atoms of whatever is selected turn pink and are now
controlled by the buttons next to “(sele)”, which is under 1IGT. Select C=color by ..ss=
secondary structure, so the helices of chain A are one color, the sheet another color and
the loops are a third color. What happens to the fasta residues at the top of the Pymol
Viewer?
6. At the command line type “select chain B”. The response is ”selection "sele" defined with
4445 atoms.” Type “center sele” and the selection is centered in the viewer.
7. At the command line type “select sheets, chain C and resI 1-100”. Notice that “(sheets)’
has appeared at the top right section of the Pymol Viewer under (sele). It has its own set
of buttons to control actions like showing, hiding, labeling and coloring.
8. At the command line type: “select GLN_BB, chain B and resI 39 and name n+ca+c+o+h”
so you can see the glutamine backbone atoms. Then type “select GLN_side, chain B and
resI 39 and name cb+cg+cd+oe1+ne2+he21+he22” and color these side-chains atoms
differently. (Note that Huntington’s disease is caused by a mutation in the gene for the
Huntingtin protein such that 40 to 80 repeats of the “CAG” codon causes the protein to
contain a string of 40 to 80 glutamine residues, ultimately leading to death of neurons.)
9. Type a command that will name your selection tryptophan_NE and will select chain B,
residue 103, atom NE1. In your command use this form for your selection: B/103/NE1.
Color tryptophan_NE blue and show as sticks.
Play around with Pymol to view different parts of 1IGT. When you’re done, save your session
(Files … Save Session As). Double-click on your saved session and you’ll see that Pymol has
reconstructed your work with 1IGT.
More on Pymol:
There is so much to do in Pymol, and this activity only scratched the surface. When you want to
do something in Pymol you can usually find instructions on the internet. For example, in google
you can type “Pymol align” to find out how to align structures.
Here are some tutorials on how to use Pymol:
http://www.youtube.com/watch?v=vDlyfk2zC-k
http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Molecular_and_Cellular_Biology/PyMol_tutorial