Installation and first use

Installation

1. Download and install YASARA

   The FoldX plugin for YASARA can be used in any stage of YASARA: View, Model, Dynamics, Structure, Twinset. YASARA View is the free version of YASARA and can be downloaded from http://www.yasara.org/viewdl.htm after free and simple registration. You will receive a download link in your mailbox shortly after registration. Installation instructions are in the mail from YASARA.

   The plugin only works from YASARA version 12.2.20 and higher. Upgrading to the latest YASARA is strongly recommended.

2. Download and install FoldX

   The FoldX plugin for YASARA requires that you have FoldX installed on your computer. For compatibility purposes you need to download the latest version (FoldX 3 Beta 5, expires in january 2013) from http://foldx.crg.es after free and simple registration for academic users.

   Commercial users should contact CRG tech transfer to acquire a license. A trial version can be obtained first.

   Install FoldX by unzipping the file you just downloaded. This will unzip two files: an executable file and a file called 'rotabase.txt'. Both are necessary.

3. Download and install Python

   On Linux and MacOSX machines Python is installed by default. Windows users can download Python from http://www.python.org/download or install it from within YASARA by clicking:

   Help > Install program > Python

4. Download and install the FoldX plugin for YASARA

   The plugin can be downloaded HERE.

   The content of the plugin has to be extracted in the yasara/plg folder (or yasara\plg folder for Windows users). Note that MacOSX Finder usually hides this folder from you, you need to right-click on the YASARA application to enter its context menu and select 'Show package contents'. After the file extraction you should have these 7 files in your yasara/plg folder:

   1. foldx.py
   2. foldxaminoacids.txt
   3. foldxanalysecomplex.py
   4. foldxbuildmodel.py
   5. foldxplotoutput.py
   6. foldxrepair.py
   7. foldxstability.py

First use

Start YASARA and load a structure. Now go to

Analyze > FoldX > Configure plugin

In the first browser window select the FoldX executable file and in the second browser window select the rotabase.txt file that came with FoldX.

As long as you don't change the location of those files or you don't delete the automatically created foldx.cnf file, this procedure has to be done only once.