Modeller

Find up-to-date instructions on http://www.salilab.org/modeller/release.html !

1. Get a license key from http://www.salilab.org/modeller/registration.html

2. Download the appropriate package from http://www.salilab.org/modeller/download_installation.html

3. Example (see Modeller site for up-to-date instructions): if you don't have sudo rights:

   in this case you need to download the tar.gz 'generic linux' version and install it as described:

   wget http://www.salilab.org/modeller/9v8/modeller-9v8.tar.gz
   tar xvfz modeller-9v8.tar.gz
   cd modeller-9v8
   ./Install
   

   Add your license key to the file /usr/lib/modeller9v8/modlib/modeller/config.py

4. Link the generic name 'modeller' to the binary into your $PATH, for example (Note the back-quotes):

   cd /usr/local/bin
   sudo ln -s `which mod9v8` ./modeller
   

5. Adapt biskit settings:

   In the latest version of biskit, Modeller.py has been refactored to adhere to the general Executor interface. The default binary name is now 'modeller'. Before it was 'mod8v2'. A different binary name (e.g. 'mod9v2') can be set up by copying biskit/external/defaults/exe_modeller.dat to ~/.biskit/ and changing the bin= parameter.

6. Test your installation:

   cd biskit/Biskit/Mod
   python Modeller.py
   

   Should yield:

   Creating /tmp/tmpUe9IOr_test_Modeller/modeller
   Running Modeller ..
   cd /tmp/tmpUe9IOr_test_Modeller/modeller ; /hal/home/grunberg/local/bin/mod8v2 modeller.top
   The modelling result can be found in /tmp/tmpUe9IOr_test_Modeller/modeller
   

   Note: A warning like this:

   'import site' failed; use -v for traceback
   

   indicates that modeller didn't find matching python libraries for its built-in python interpreter. This doesn't matter for the Biskit.Mod functions.

Usage:

see Biskit.Mod.Modeller

Configuration:

see biskit/external/defaults/exe_modeller.dat