Download Jmol answers

Jmol worksheet
Exercise 1: Jmol controls and style schemes
 Download the pdb-file of the amino acid L-leucine from the Klotho database:
http://www.biocheminfo.org/klotho/
 Create space-filling, ball-and-stick and wireframe representations of the
molecule
 Copy and paste screen shots of your Jmol visualization into the form below
(select Jmol window, Alt+PrintScreen, Ctrl+v)
 Each of these representations provides specific information about the molecule
– specify what this is.
Style
Image
What information does this give
about the molecule?
Space-filling
Molecular volume represented
by the van der Waals radi of the
constituent molecules.
Ball-and-stick
Bond order and bond angles
Wireframe
Bond order and bond angles,
often more clear than the Balland-stick style when viewing
large molecules
Exercise 2: Protein analysis

Download the PDB file 3cpa (Carboxypeptidase A) from PDB database:
o http://www.rcsb.org
o http://www.ebi.ac.uk/msd-srv/msdlite/ (European mirror at EBI,
usually faster)
Questions:
a) What are the amino acid residues at the N and C-termini of the protein?
N-terminus: ALA1
C-terminus: ASN307
Hint: Display backbone using Cartoon style:
Style > Structures > Cartoon
Color strands by secondary structure succession:
Color > Structures >
Cartoon > By Scheme > Group
b) How many helices does the protein have?
8
c) How many beta-strands and beta-sheets does the protein have?
1 sheet that consists of 8 strands
d) What is the distance from the C-terminus to the N-terminus in nm?
3.972 nm
Bonus Exercise: 3D visualization
Try out the stereo 3D viewing feature in Jmol.
Open the L-leucine structure and turn on Cross-eyed viewing:
Style > Stereographic > Cross-eyed viewing
For more instructions on stereo viewing see the tutorial at:
http://spdbv.vital-it.ch/TheMolecularLevel/0Help/StereoView.html
Additional background information and web tutorials:
http://jmol.sourceforge.net/
http://www.bluffton.edu/~bergerd/classes/jmol.html