Hi Conrad, I read the paper Intersurf: dynamic interface between proteins Nicolas Ray, Xavier Cavin, Jean-Claude Paul, Bernard Maigret Journal of Molecular Graphics and Modelling, 23 (205) 347-354 It addresses 3 problems: how to find a surface interface between 2 proteins, ways to color such a surface, and how to flatten that surface into two dimensions. The surface calculation was a neat algorithm -- take the Delauney tetrahedralization of all atom positions from both proteins, then find tetrehedra with vertices from both proteins and cut those tetrahedra in half. The tetrahedra are cut in half with one or 2 triangles using vertices on tetrahedron edges that connect an atom in one protein to an atom in the other protein. The vertices are placed midway between the atoms moved in by their vdw radii. They proposed 2 ways of coloring the surface. One colored vertices by how far apart the atoms were in the two proteins that were used to create that vertex. Red to blue shows short to long distances. The other coloring shows types of possible interactions between the two residues associated with the two atoms for the tetrahedron edge that the surface vertex splits. They gave different colors for predicted hydrogen bonding, hydrophobic packing, pi ... X, pi ... pi, same charges, opposite charges. Not sure what the pi bonding notation means. They also described how to flatten the 3-dimensional to a 2-dimensional surface with one to one correspondence between vertices and edges. Their method tried to come as close as possible to a conformal map. Conformal means the angles of the triangles stay the same to the extent possible. These calculations took a few seconds on 2000-5000 atom proteins. Here's my assessment. I think the concept of showing a protein interaction interface and coloring it to show interactions sounds useful for protein- protein interaction people. I think the flattening into 2 dimensions is probably not useful. Conformal maps greatly distort the area of the surface if it has curvature (you've seen the maps where Greenland is bigger than Africa, Americas, Asia and Europe combined). So the flattened surface is going to be hard to recognize as the interface, unless it is already pretty flat. If it is already pretty flat you might as weill just look at the 3-d surface. If we wanted to do something with interface surfaces I would suggest talking to Tanya Korteme. We already have all the infra-structure to create the surfaces. I would not use the Delauney surfaces, instead just use MSMS surfaces on both proteins showing only the parts associated with atoms in one protein that are within 5 angstroms of atoms in the other protein. The zone calculation code I wrote for multiscale could do that fast. We could offer a range of atom colorings that map onto the surface (hydrogen bonds, distance to nearest atom in other protein, charge complementarity, etc...). I don't have time or enough interest to work on this project. But perhaps someone else will. We have talked about collaborating with Tanya Korteme in the past and this would be a good opportunity. Tom