Introduction

This plugin enables you 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 PyMOL, it can be obtained here. You should also have Python 2.7+ installed on your machine.

Installation

Automatic installation from a terminal (Mac + Linux):

• Download and unzip the file PySwissSidechain.zip in a directory of your choice.
• Go to the new PySwissSidechain directory and run the installation script (# ./install.sh).

You will be asked to give the path to your PyMOL application.

On Mac, if PyMOL is in the Applications folder, this should be something like: "/Applications/MacPyMOL.app/".

On Linux, give the path of the directory containing the pymol/ folder. This is typically the directory where you have untarred the pymol-vxxx-Linux-xxx.tar.bz2 file.

Manual installation (Mac + Linux + Windows):

• Copy all files from the fragments directory into PYMOL_PATH/pymol/data/chempy/fragments/.
• Create a directory PYMOL_PATH/pymol/data/chempy/SwissSidechains.
• Copy the two files from the SwissSidechains directory in this new directory.
• Copy mutagenesis1.py into PYMOL_PATH/pymol/modules/pymol/wizard/.
• Copy PySwissSidechain.py into PYMOL_PATH/pymol/modules/pmg_tk/startup/.

Note that on Windows, the PYMOL_PATH would typically look like "C:\Program Files\PyMOL" and pymol is sometimes spelled PyMOL depending on the version of PyMOL you are using.

Running

Plugin Menu (on Mac,version 1.0 to 1.4)

Go under the Plugin->PySwissSidechain:

• Enter the residue you want to mutate as: Object//Chain/ResNumber/ (e.g., complex//E/82/)
• Enter the new residue code (e.g., HLEU)

Command line

Use the command:

  Mutate Object//Chain/ResNumber/, Newres

For instance, to mutate residue number '82' on chain 'E' in object 'complex' into Homoleucine (HLEU), write:

  Mutate complex//E/82/, HLEU

You can then choose between the different rotamers by clicking on the arrows at the lower right corner (same as standard Mutagenesis). Click 'Apply' and 'Done' to validate your mutation.

If you only have one object, you can simply write:

  Mutate Chain/ResNumber/, Newres

For MacPyMOL1.5+, you need to explicitly load the plug everytime you open MacPyMOL:

  run PYMOL_PATH/pymol/modules/pmg_tk/startup/PySwissSidechain.py

or you can rename MacPyMOL applications to MacPyMOLX11Hybrid.

D-amino acids

Use the Pymol plugin D_PySwissSidechain.zip.

Instal it in the same way as the PySwissSidechain plugin.

The plugin appears under Plugin->D_PySwissSidechain.
The command line uses 'D_Mutate' instead of 'Mutate'.

Older versions of MacPyMOL (0.99)

For older versions of PyMOL (such as 0.99), download these two files PySwissSidechain.zip and D_PySwissSidechain.zip. You also need to manually load the plugin by running the command:

  run PYMOL_PATH/pymol/modules/pmg_tk/startup/PySwissSidechain.py

everytime you open MacPyMOL.