Hi Paul, You mentioned coloring continuously (gradual shading over a color range) based on distance from a point or axis, as can be done with Color Surface. There is no tool that does exactly what you describe, coloring a molecular surface continuously based on vertex distance from some set of atoms, but there are some possibilities that may do part or all of what you had in mind: (1) The first two ideas do not use the surface vertex coordinates. Instead, atoms can be selected based on their distances from another set of atoms, and then the surface patches that go with those atoms can be colored. These also do not provide shading over a range of colors. You could use successively more stringent cutoffs and get a series of colors that way, but they would not blend smoothly into each other. (a) select atoms in one chain within a certain distance of atoms in the other chain, color them, repeat with smaller cutoff if you want to use multiple colors (must go larger->smaller as the opposite direction will overwrite the previous colors). If you use commands rather than the menu, you can just specify and color in a single step without selecting. Example commands: open 2r4s; surfcat receptor :.a; surfcat antibody :.h:.l surf receptor color pink,s receptor & antibody za<5 color red,s receptor & antibody za<4 (b) use Find Contacts/Clashes (or findclash command) to select atoms in one chain that contact atoms in the other chain, color them. The advantage over (a) is that this uses different VDW radii for different atom types and allows compensation for hydrogen bonding. Perhaps (a) is better if you want to use multiple colors, (b) if you want to know which atoms are really contacting. Using the same example structure as in (a), for example, start "Find Clashes/ Contacts" (under Tools... Surface/Binding Analysis). Select chain A (for example, command "sel :.a"), click "Designate" in the top section of the clash dialog. In the parameters section, click "contact" to set suggested values for identifying contacts. In the bottom section, choose only the coloring option and set the color as desired before clicking "Apply." If you previously tried (a) and you don't see a color change in the surface when Apply is clicked, try using the command "~color,s" to remove those previous colors. (2) Intersurf does continuous coloring, but as you mentioned, the surface is chunky and currently there is no way to increase its vertex density. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 21, 2007, at 4:03 AM, <Paul.Pillot@ac-nice.fr> wrote:

Hello, I can color a surface according to the distance from a single point or a plane, but is it possible to do it according to the distance from a selection (eg an other chain or molecule) ? My aim is to show the contacts between an antibody and an antigen. I tried the tool intersurf for doing it, but the result is pretty crude (low definition of the surface compared to the usual surfaces available). Thanks in advance, Paul