Objective

Zahnd et al. 2007. A designed ankyrin repeat protein evolved to pico molar affinity to Her2.J. Mol. Biol. 369: 1015-1028

Your task is to replicate the figure shown below in PyMOL. It is not just a matter of making a cartoon and highlighting side chains. Some of the atoms in the side chains are missing exposing only from CB... onwards. As well, the side chains are a different colour than the helices so you will have to figure out a few atom selections to achieve this. The cartoon helices are two different colours on the inside and outside and the whole thing is ray traced. The brown colour might be tricky as well.

Starting out

Being by opening PyMOL and typing

   fetch 2jab

You don't have to worry about putting labels on the figure like they have, as they were done in a drawing program like Adobe Illustrator, after the fact. Not that Q45 in the figure is actually E45 in the structure.

Figure 3 Crystal structure of H10-2-G3. The overall structure is shown in ribbon representation in front view, looking towards the putative binding surface. The side-chains of residues that had been randomized in the synthetic library are drawn in ned. Side-chain of framework residues that had been mutated in the course of affinity maturation are drawn blue Note that only ionic of the side-chains that have been drawn are labeled.