The modify residue panel

The modify residue panel (figure 10.29) offers the following operations:

Image proteinOptimizerModifyPanel
Figure 10.29: The modify residue panel

The atoms in the modeled residue will be assigned temperature values as described in Protein coloring to visualize local structural uncertainties. That means that atoms with steric clashes will be colored bright red when visualized using the "Color by Temperature" color scheme (Visualization styles and colors).

What is seen during a modification?
Modifications to a residue take into account all visible molecules in the residue's neighborhood. For example, a mutation in a binding pocket may choose different rotamers as the bound ligand is toggled on and off (figure 10.30).

Image proteinOptimizerVisibleAvoidance
Figure 10.30: Left: A ligand (yellow) is visible. The side chain is placed taking the position of the ligand into account. This leads to a clash (red) between atoms in the protein chain. Right: The ligand is toggled off, and the side chain is rebuilt. It can now occupy the space previously occupied by the ligand, removing the earlier clash.