How to install HIP under linux:

1. Make sure you have installed "stride", a secondary structure assigner. (http://binfo.bio.wzw.tum.de/groups/frishman/software )

2. Make sure you have installed "msms" (www.scripps.edu/~sanner/html/msms_home.html)

3. Change to your desired directory $home and enter "tar -xvf HIP.tar"

4. Make sure the executables under libproteingeometry-2.0.beta directory are executable; otherwise, you need to re-compile them.

5. Modify $stride, $geometry, $msms_exe_dir to where you install them in cal_contactarea.pl

6. Modify $home to where you install the scripts in predict_cylinder_contactarea.pl

****************************************************************
How to run the scripts:

a. cal_contactarea.pl: calculate the precise surface contacts between helices (Voronoi surface, solvent-accessible surface and molecular surface)

To run, enter "cal_contactarea.pl \$absolute_path/\$pdb_name.pdb (-o \$absolute_path_output_dir)". The output directory is optional, default being current working directory, and the output file is $pdb_name_cal_contactarea.out and $pdb_name_cal_isolate_helix.out (for each isolated helix).

b. predict_cylinder_contactarea.pl: predict the contact area between helices within a pdb file based on the geometry of cylinders

To run, enter "predict_cylinder_contactarea.pl \$absolute_path/\$pdb_name.pdb (-o \$absolute_path_output_dir)". The output files are $pdb_name_predict_cylinder_contactarea.out and $pdb_name_predict_isolate_helix.out (for each isolate helix cylinder).