Residue Electrostatic Interaction Strength Visualizer
Created by Greg Grothaus
Contact Jonathan Myers (jonmyers@vt.edu) for assistance

Installation:
This requires awk, grep, sed, a c++ compiler and python.  It should work out of the box for most any linux distribution.
To install, simply type:
$ make

Usage:
$ ./conStrength.py <pkint file> <g file> <pdb file> <minimum connection strength kcal/mol>

The .pkint, .g, and .pdb files can be acquired from the H++ website at http://biophysics.cs.vt.edu/H++/.  Once run has been completed select "View all files generated for this run: Listing" and all three files will be listed.
The minimum connection strength is up to the user.  Setting this number to zero will show the connections between all residue pairs, a difficult to interpret image.  The higher the number, the fewer the number of visible interactions.  All interaction strengths will be denoted by visible edge thickness and color, distributed across the range of interaction strengths selected.  That is, if the smallest interaction strength above the threshold is X, the interaction with strength X will have the least thick edge possible and the reddest edge possible.  The interaction with the highest strength will have the thickest and greenest edge.  These color choices were made as small red lines are easier to see on a white background than small green lines.

Output:
Output from the above command will be to the file "drawscript".  This script can be loaded into rasmol by typing the following into the rasmol prompt:
# rasmol <pdb file>
RasMol> script drawscript

You can also load the script through standard in:
$ rasmol <pdb file> < drawscript

Alternatively, if rasmol is directly on your path, comment out line 21 and uncomment line 20 in conStrength.py, and conStrength will automatically run rasmol for you.

Example:
In the /example directory there is a pre-processed protein that we will use as an example:

$ ./conStrength.py example/1qhj.pkint example/1qhj.g example/1qhj.pdb 0.6
$ rasmol example/1qhj.pdb
RasMol> script drawscript


