Installing SOMO:

1) Download somo_last.tar.gz file from this website
2) Place it in the directory where you want to store somo, for example /home/mrc/somo
    % mkdir /home/mrc/somo
    % cp somo_last.tar.gz /home/mrc/somo
    % cd /home/mrc/somo
    % tar xzvf somo_last.tar.gz
3) After this, you will need to set your $SOMO_PATH variable to point to the directory where you installed SOMO, eg
    % setenv SOMO_PATH /home/mrc/somo
 
4) You have to point the PATH variable to the somo path. In our example, you do that by doing
    % setenv PATH ${PATH}:${SOMO_PATH}/bin

5) You refresh your variables by doing:

% rehash or reopen a new terminal window or do %csh

You can permanently set this variable by adding the lines :
setenv SOMO_PATH /home/mrc/somo and
setenv PATH ${PATH}:${SOMO_PATH}/bin

to your .cshrc file in your home directory ( $HOME or ~/ or in our example /home/mrc )

Alternatevly and depending on your shell you might need to modify this commands to suit your own shell (such as bash)

  
Running SOMO

1) Cd to the directory having your pdb files, for example:
    % cd ~/hydrodynamic-models/
    % cp $SOMO_PATH/somo.cfg ./

If you start from a file in PDB format, you should follow the following steps:

2) run asab1 to generate the accessible surface area data needed by SOMO and usually (unless otherwise stated) stored in the socalled "provaly" files.
    This you can do by either:
    a) running asab1 directly on the PDB structure by
        %asab1
        inputs: 2, 1.4, 10,
        then select PDB input filename, output filename (for example "test"), and integration step (usually 1)
        As output, asab1 produces three files: test, test1, test2 (or as default provaly, provaly1 and provaly2).
   
        Then you should invoke somo by doing"
        % somo test
        or %somo provaly (if you used default output filenames)
    b) Alternatively, you can directly run somo by
        % somo
        And somo will invoke asab1 for you. Then you should follow the steps undelined above for running asab1 and use default output filename.

4) You can either run somo with the options described in the file "somo.cfg" that you copied before in the directory (you can edit this file with vi, nedit, emacs or fetch) or input each option by hand.
    The output from somo is in either BEAMS or HYDRO formats, depending on your specifications.

5) After SOMO has been run successfully, you can run 'supcw' or 'hydro' to calculate the hydrodynamic parameters of the models, such as rotational diffussion coefficient, and sedimentation coefficient.

Any problem with the installation, mail me at marcnol@chem.gla.ac.uk or marcelo_nollmann@yahoo.fr

Marcelo Nollmann, July 2003.