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ICM-Browser

ICM-Browser is the free version of Ruben Abagayan's ICM program. There is lots of interesting functionality in there. Biskit right now only wraps a single method -- the calculation of CAD (Contact Area Difference) as a better behaved alternative to the classic RMSD measure for structure comparison.

To install the program...

  1. Download a pre-compiled package for your platform from http://www.molsoft.com/icm_browser.html

    You can choose between rpm and a self-extracting installation script. The latter may be the better option -- at least in my case, the rpm installed ICM in a very unusual location (/usr/icm-browser... ).

  2. Install the program

    Excute the sh script or install rpm.

    Mac OS-X users: unpack the zip file and move icmbrowserpro.app into /Applications

    Note:

    The installation doesn't seem to tolerate any other location than /usr/. Just go ahead with that and move the icm folder afterwards to, e.g.,:

    sudo mv /usr/icm-browser-pro* /usr/local/lib/
    cd /usr/local/bin
    sudo ln -s /usr/local/lib/icm-browser-pro-*/icmbrowserpro .
    sudo rm /usr/local/lib/icm-browser-pro
    
  3. Set $MOLBROWSERPROHOME environment variable:

    for example, add this line to ~/.zshenv or ~/.bashrc:

    export MOLBROWSERPROHOME=/usr/local/lib/icm-browser-pro-3.5-1l
    

    .tcshrc or .cshrc example:

    setenv MOLBROWSERPROHOME /usr/local/lib/icm-browser-pro-3.5-1l
    

    under Mac OS-X:

    export MOLBROWSERPROHOME=/Applications/icmbrowserpro.app/Contents/Resources/icm

  4. Optional: Configure Biskit for non-standard binary

    In case your icm binary is not actually called icmbrowserpro or not in the $PATH, you need to tell Biskit about the new location:

    • Copy the file exe_icmbrowser.dat from biskit/external/defaults/ to ~/.biskit/.

      The local copy in your home .biskit will overide the default configuration.

    • Change the bin= parameter to the correct binary value

    • You may also provide an explicit value to the MOLBROWSERPROHOME= parameter to make Biskit independent of your shell environment.

  5. Test the icmbrowserpro / Biskit interface:

    cd biskit/Biskit
    python IcmCad.py
    

    Should yield something like this:

    Loading PDB...
    Starting ICM
    Running
    Result:  [8.8603529999999999, 9.0315890000000003, 8.5055429999999994]
    

Usage:
see IcmCad
Custom configuration:
see biskit/external/defaults/exe_icmbrowser.dat
(described in detail above)