Select "Tools" Category and add the directory containing the
SwissSidechain folder to the "Locations".
The SwissSidechain module now should appear under Tools->Structure
Select the residue you want to mutate.
Go to Tools->Structure Editing->SwissSidechain/.
Select one of the non-natural sidechains of SwissSidechain and
Select one of the rotamers and click Apply'.
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.
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