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Introduction

This module enables users to mutate any residue of a PDB structure into one of the non-natural L- or D-sidechains of the SwissSidechain database.

If you do not have UCSF Chimera, it can be obtained here.

Installation (Chimera 1.5+)

  • Create a new directory that will contain the plugin.
  • Download and unzip the file SwissSidechain_chimera.zip in this new directory.
  • Open Chimera and go to Favorites/Preferences.
  • Select "Tools" Category and add the directory containing the SwissSidechain folder to the "Locations".
The SwissSidechain module now should appear under Tools->Structure Editing menu.

Running

  • Select the residue you want to mutate.
  • Go to Tools->Structure Editing->SwissSidechain/.
  • Select one of the non-natural sidechains of SwissSidechain and click 'Apply'.
  • Select one of the rotamers and click Apply'.
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Command line

Use the command 'swapnaa':

  swapnaa Newres #Object:ResNumber.Chain

For instance, to mutate residue number 82 on chain E in object 0 into Aminobutyric acid (ABA), write:

  swapnaa ABA #0:82.E

'swapnaa' automatically selects the most favorable rotamer, as predicted by Chimera.

D-amino acids

This plugin enables you to mutate a residue to both natural and non-natural D-amino acids of SwissSidechain. Download the D_SwissSidechain_chimera plugin.
For installation, proceed in the same way as for the SwissSidechain plugin.
Use the command 'swapdaa' instead of 'swapnaa' or select the D_SwissSidechain module under Tools/Structure Editing/ to mutate residues.

Word of caution:

The current version of the SwissSidechain module for UCSF Chimera only includes contiguous dihedral angles used to define rotamers. For sidechains with non-contiguous dihedrals, such as 0A1, only the contiguous dihedral angles have been included in the rotamer library. If you work with these sidechains, you should either check manually the additional dihedral angles, or use our PyMOL plug-in.