LIGPLOT is a pretty neat program written by Andrew Wallace and Roman Laskowski
that not only finds and draws hydrogen bonds between a ligand and its
protein, but then manages to make a 2d projection without plastering a lot
of atoms on top of each other.
Their documentation is at : http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html
All I'm offering is a script for setting up local pointers so that you can make your first plot.
Then you are on your own. And on an alpha, as there's no SGI version yet.
So, go to a directory where you have a PDB file containing a protein and a ligand (eg myfile.pdb, with the ligand at residue 499), then execute the following commands to see a pretty plot :
% source /home/markh/bin/ligplot/ligplot.setup % cp $ligdir/ligplot.prm . % ligplot myfile.pdb 499 % ghostview ligplot.ps
Personally, I have 2 aliases set up as follows :
% alias ligset 'source /home/markh/bin/ligplot/ligplot.setup' % alias ligprm 'cp $ligdir/ligplot.prm .'
Note that the output file by default is always called ligplot.ps.
If ghostview doesn't work for you, try 'gs' or 'showps', or 'gimp'.
At BMC you can also run ligplot through the web interface Molray.
Mark Harris, 30 Sept '99