groups. Check that all cross-linked residues on the model
structure are the correct residue type.
Missing atoms—residue sidechains may be missing atoms
for various reasons, such as poor electron density from protein
crystallography. While checking the residue numbering and
type, also check if any of these sidechains are missing atoms
(see Note 3). By default, proteins opened in PyMOL version
2 and above will be represented in cartoon format. To display
full atomic information, you will need to select the residue of
Fig. 2 Visualization of protein structures using PyMOL. (a) Ribbon representation of the PDB 1WBJ tryptophan
synthase. (b) Display of atomic bonds for a selected residue
226
Andy M. Lau and Argyris Politis