Mutating Residues in PDB Files

"Mutation" means changing one or more amino acids or nucleotides in a protein or nucleic acid chain. Mutation of a 3D model is modeling, and hence not within the capabilities of Protein Explorer. However, it is quite easy to "mutate" a protein 3D model (PDB file) using DeepView (also called SwissPDB-Viewer), and then explore the resulting mutation structure in Protein Explorer.

To download and install DeepView, look in the DeepView section of the World Index of Molecular Visualization Resources (

The following instructions were written for Windows DeepView version 3.7-beta2. If you are using a different version, or a Macintosh, some details may vary.

  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.

  4. Click the Mutate button (in the top row of large square buttons).

  5. Click on the residue you want to mutate, and a menu of the 20 amino acids will open. Release the mouse button and slide the mouse away from the menu, and the current amino acid will be highlighted. Click on the target amino acid for the mutation of this residue -- the new sidechain appears immediately!

  6. Notice the rotamer message in red that appears just below the top row of large square buttons. There are a number of possible conformations of the mutated sidechain, called "rotamers". Automatically, a rotamer has been selected with the lowest energy (fewest collisions and most favorable hydrogen bonds, if any). There may be several rotamer positions with equally low energy. Notice the score; negative scores are favorable and positive scores are unfavorable. Click on one of the small triangles near the red rotamer message to step through the possible rotamers, noting the energy score for each one. As you do this, notice the green and pink dotted lines, which represent favorable hydrogen bonds or unfavorable steric collisions, respectively. Choose any one of the lowest energy rotamers that you prefer.

  7. Click the "Mutate" button again, and either accept or discard the mutation.

  8. Use the File menu to Save the one Layer you have loaded. This saves a PDB file you can load into Protein Explorer.