Install YASARA and its FoldX plugin

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Part of Protein Structure Analysis training

Source: http://foldxyasara.switchlab.org/index.php/Installation_and_first_use

Installation

  1. Download and install YASARA
    YASARA View is the free version of YASARA and can be downloaded from our website.

The FoldX plugin for YASARA can be used in any stage of YASARA: View, Model, Dynamics, Structure, Twinset.

  1. The plugin only works from YASARA version 12.2.20 up to version 17.1.28
  • Download and install FoldX
    The FoldX plugin for YASARA requires that you have FoldX installed on your computer as a 'stand alone' program. For compatibility purposes you need to download the latest version (FoldX 4) from http://foldxsuite.crg.es after free and simple registration for academic users.
    Commercial users should contact [1] to acquire a license.
    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.
  • 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
  • Download and install the FoldX plugin for YASARA
    The plugin can be downloaded from our website.
    The content of the plugin has to be extracted in the yasara/plg folder (or yasara\plg folder for Windows users). After doing that you should have these 7 files (among many others) 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, such as 2AC0.sce. 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 overwrite the foldx.cnf file (be careful when unzipping a new version directly in the plg folder), this procedure has to be done only once.

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