The modify residue panel
The modify residue panel (figure 10.29) offers the following operations:
- Mutate a residue. The current amino acid is selected in the drop down box. Select a new amino acid to mutate the residue. The mutated residue always has the best minimized rotamer.
- Rebuild a residue that is missing side chain atoms. To do this, click the rebuild button. The residue is rebuilt completely, without taking existing positions into account.
- Change the protonation state. The current state is shown in the drop drop down box. Select a new state to change the protonation.
- Choose a rotamer for a residue. Rotamers are minimized when selected.
- Flip a residue. Asparagine (ASN), Glutamine (GLN) and Histidine (HIS) residues contain pairs of atoms that are often hard to distinguish in protein crystal structures. The flip button swaps these pairs of atoms, but keeps their coordinates fixed. A flip may be required if i) rebuilding the residue favors the flipped conformation, ii) flipping improves the local hydrogen bond network, or iii) hydrogen atoms clash without the flip.
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).
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What is seen during a modification?
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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.