Pymol Exercises:
BMS 791A Fall 2008
Today we will look at the crystal structure of Pyrobaculum aerophilum (Pae) SurEα, a homolog of survival
protein E (SurEα), an acid phosphatase, using the program called PyMol. The structure reveals a dimer in the
asymmetric unit of a P3121 cell. This is an example taken from Cameron Mura’s homepage:
http://mccammon.ucsd.edu/~cmura/PyMOL/pymol_mainFrame.html
1. Get the files we will need and save them onto the desktop:
a. Login to one of the CRC computers.
b. Open Safari by clicking on the compass icon.
c. go to http://people.chem.umass.edu/jhardy/BMS2008.html
d. From Oct9 Reading download map (map2.xplor) ps (ps.pdb) & cal (calmodulin.pse) onto the desktop.
2. Open MacPymol and load the protein structure:
a. Open MacPymol by clicking on the MacPyMOL icon.
b. In Pymol FileOpen ps.pdb
3. View Electron Density Maps:
a. Show PS as lines only. Color by element using your favorite scheme.
b. Load the electron Density map (map2.xplor) by File  Load  map2.xplor
c. Turn the background to black using DisplayBackground  Black.
d. Select Wizard  Density. A new bar called w1_map2 will appear in the Names Panel.
e. PkAt (single left click) at the atom you want to see density for
f. Use slab and move to get a clear view of the residue you are centered on.
g. Can you see any clear but unattached spheres of density? What are those?
h. Find and alpha helix and look at the tube of electron density that is formed by a helix. (Draw a
cartoon and color by secondary structure, if necessary, to help you find the helices.) Note that the
cartoon really does not match the density so it only makes sense to show sticks or lines.
i. What do you notice about the density for the loop regions?
j. Turn off the molecule and only look at the density. Don’t cheat. Can you locate any secondary
structure? Can you see any large aromatic residues that would help you determine where you are in
the sequence.
k. OPTIONAL: An alternative to the Density wizard is to use the command : PYMOL> isomesh
msh2,map1,1.0,(chain A),3.0 This command tells Pymol to display an isosurface−mesh contoured
at 1.0 Å in a brick about chain A with a border of 3.0 Å.
4. Align two structures
Remember that commands must be typed exactly as written including spaces. In these exercises, you don’t have
to type PYMOL>, that is written to indicate that what follows should be typed at the PyMol prompt. Also,
remember the PyMol hierarchy:
/object−name/segi−identifier/chain−identifier/resi−identifier/name−identifier
a. I have prepared calmodulin.pse which you can download from the course website. It contains three pdbs:
1F70: NMR structure of N-terminal domain
1CLL: X-ray structure of calmodulin+calcium
1CDL: X-ray structure of calmodulin+calcium+peptide (edited to contain one calmodulin)
b. Open the sequence viewer so that you can get a sense of what you are looking at. Arrange the view so that
you can see all three molecules. I suggest looking at them in cartoon view.
c. Try to globally align 1CLL and 1CDL using the align command. The default for align is align target, source.
The target is the structure that will move the source is the structure that will stay stationary. Try this
command:
PYMOL > align 1CLL, 1CDL
What happens? Is this successful? Why not?
d. In order to align these two molecules it is necessary to define which part of the protein you want to align.
Decide which regions should be aligned and align them using the align command specifying which
residues you want to align. For example if you want to align the entire structure using residue26-29 only
you could issue one of these commands. Make sure you understand why they both work.
PYMOL > align /1CLL///26-29, /1CDL///26-29
PYMOL > align /1CLL///26-29/n+ca+c+o, /1CDL///26-29/n+ca+c+o
e. Now align all three structures. Show the sticks for the important residues for binding calcium, peptide and
making interdomain contacts. What happens when calcium binds to calmodulin? What happens when
peptide binds to to calcium-bound calmodulin?
f. Close what you have done and reopen the original calmodulin.pse. Use the pairfit wizard to align two of the
structures. This tool can be useful if the sequences are complicated or if you can visually see what you
want to align.
5. Make a simple Movie of rotation in PyMol
Now we want to make a movie for a presentation. Using the Mac version of PyMol we can easily make a movie
and save it in quick time format. Quicktime movies can be inserted into Powerpoint presentations. We will
make a movie of the rocking calmodulin or any other protein you are interested in. If you want to work on
another protein just grab it from the pdb. In this exercise we will enter the commands for the movie manually,
but in the future when you want to make a more sophisticated movie you can also make the commands in a
script called movien.pml and then run the script to generate the movie by using the command that includes path
of where movien.pml is located.
PYMOL >@/Users/yourname/Desktop/movien.pml
a. Put a copy of the pdb you want to use on the desktop. Use right click and select Get Info on it to find out the
path to the file. It will likely be /Users/yourname/Desktop/yourchoice.pdb
b. First you want to set up your movie. You must define the actors. The command below says we are going to
make a movie with one actor “yourchoice” and set it to the first state. This movie will have just one state.
PYMOL >load /Users/yourname/Desktop/yourchoice.pdb, state = 1
c. Make your molecule look like you want it to look. Color it appropriately, draw sticks or surface or whatever
you like. Leave it in the orientation you want to have in the movie.
d. We need to next say how many frames we want in our movie. Because we want a short movie that we can
calculate during class we will chose to have 60 frames. We can make a longer movie by increasing the
number of frames. The mset command below defines the movie 1 x60 says to hold state 1 for 60 frames.
PYMOL >mset 1 x60
e. You will set up your movie using the movie.rock command. In the mset command above the total number of
frames is 60. It is important the second number in mset is equal to the number of frames in your movie.
The third numbers is the number of degrees that you want the movie to rock.
PYMOL> movie.rock 2,60,10
f. Now we want to save the movie. File  Save Movie As  Quicktime  for now chose the defaults set the
save name. Now wait for it to calculate. You should see a file called whateveryounamedit.pml.tmp. When
the movie is finished making it will become whateveryounamedit.pml and you can click on it to watch it.
g. In class DO NOT use this command because this dramatically increases the amount of time it takes you to
calculate a movie but if you want to make a nicer looking movie where the frames are ray traced, select
Movie  Render Frames.