DeepView/Mutating Amino Acids

DeepView is a free molecular modeling program available for both Windows and OS X. Here are instructions for using DeepView to mutate an amino acid.

Caution: DeepView cannot predict changes in overall protein conformation after mutating amino acids, and it is unlikely that any existing program can do this reliably. Therefore, mutating one or more amino acids in an existing protein model will allow you to visualize the mutated sidechains in the context of the wild-type protein structure, but the resultating mutated model may not reflect changes that such mutations may induce in protein structure.

The following instructions were written for DeepView 4.1, current in May, 2015 (released October, 2012).

1. Use DeepView's File menu item "Open PDB File" to load your molecule.
2. If you can find the residue you want to mutate by inspecting the structure, you can skip this step. If the Control Panel window is not showing, use the Window menu to open it. This allows you to see the sequences of the protein chains. Hold down the shift key and click in the column "show" -- the molecule should disappear. Find the residue you wish to mutate, and click in the "show" column to make just that one residue appear.
3. To confirm that you have the correct residue, click the identification button (top row of large square buttons, near the middle of the row, with a large question mark in it), then click the residue in the 3D image. An identifying label should appear next to the residue you clicked.