Viewing the models

We will now view the models you have built using PyMol.

Start PyMol, and load the PDB file of the model, as instructed on the previous page.

Viewing by secondary structure

• If the protein is not displayed as a cartoon, then, next to all in the menu on the right, click S, hover over as and then click cartoon.
• Now, next to all in the menu on the right, click C, then click by SS and click the first colouring option where Helix is in red.
• The cartoon image and colouring scheme in which red represents α-helices and yellow represents β-strands makes it very easy to get a feel for the structure you are looking at.
• View both models at the same time and compare them. You will notice that model2 is rather larger than model1 - remember that we used a template that matched over more of the target so we were able to build a more complete model.

Viewing by sequence location

• Change the colouring scheme for each model: next to all in the menu on the right, click C, then click spectrum and then rainbow.
• The model will now be coloured in a rainbow with blue at the N-terminus and red at the C-terminus. This makes it easier to compare the two models.

Viewing hydrophobic residues

Now we are going to look at where the hydrophobic residues lie in the two models.

For each model in turn:

• Change the colouring to white: next to all in the menu on the right, click C, then hover over 'grays' and click white.
• Change the representation to space-filling: next to all in the menu on the right, click S, hover of as, then click spheres.
• Now we are going to select the sidechains of the most hydrophobic residues: At the PyMol command prompt, type the following:

select hphob, resn ile+leu+val+phe and sidechain

• In the menu on the right, a new line will appear labelled (hphob) - this is the selection of residues you just made.
• Next to (hphob) in the menu on the right, click C, hover over greens and then click green.

Once you have compared the models, click here for some discussion.