Hi Ki, I'll answer in two parts, (A) how to tell Chimera that certain water molecules should be included with the protein when drawing a surface (B) how to show only part of the surface that forms a binding site or pocket (A) Chimera automatically puts atoms into groups it thinks are reasonable for surface calculation. This default approach keeps water molecules and ligands outside of the protein. To make a surface that combines other molecules together with the protein, use the command "surfcat" to specify the group and then "surface" to display the surface of the group. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html For example, the surface for 1nzy automatically includes the protein part of chains A,B,C. Let's say you wanted it to enclose the protein part of chains A,B plus 367 and 402 in chain "water" (in a different structure, the waters could be in the same chains as the protein residues, or in chain "het"). surfcat mysurface protein & :.a-b | :367.water,402.water surface mysurface This example is a little complicated - the reason for including the "protein &" is that chains A and B include ligand molecules, not just protein, and I didn't want the surface to enclose them. It might be simpler for your protein. If you want all the protein in your model plus a couple of waters, you could just select the two waters with Ctrl-click on the first, Shift-Ctrl-click on the second, then use: surfcat mysrf protein | sel surface mysrf (B) I should mention here are many different ways to do the same things in Chimera. The following things could also be done using selection from the screen and the Actions... Surface menu. If you know what residues line the pocket, you can just display the surface for those residues, for example: ~surface surface :64.b,90.b,114.b,137.b,145.b Or, if there is a ligand in the pocket, or an atom in the protein or a water that is approximately in the middle of the pocket, you can use it to define a zone: surface :bca.b z<6 & mysurface (show surface for residues with any atoms within 6 angstroms of residue BCA in chain B and that are in the "mysurface" group) If the surface is displayed already, you could hide the part that is outside of the zone: ~surf :402.water za>8 (undisplay surface for atoms farther than 8 angstroms from water 402) Currently zones are based only on atom-atom distances; there is no way to define them using atom-surface distances, so sometimes it takes more steps of displaying or undisplaying atomic surface patches (with surface/~surface or using the menu) to show just the part you want. 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 Jun 24, 2007, at 12:23 PM, Ki Kim wrote:

Hello, I would like to know what is the best way to draw the surface of the binding site of a protein. I would like to add some water molecules to the protein and treat these water as part of the protein. Thank you for your help. Sincerely, Ki Kim