On Mar 17, 2008, at 9:56 AM, Francesco Malatesta wrote:
Hello, could anyone help me out with this problem. I would like to exclusively colour interface residues in a dimeric protein represented as spheres or surface. Is this possible? Thank you very much Francesco Malatesta
Hi Francesco, Of course - there are so many different ways you could do it, I'm not sure where to start! Also, I don't know if your structure is opened from two PDB files, or one PDB file with a different chain ID for each monomer. You could do it either way, but in my examples I will assume you have one file with protein chains A and B like structure 1tzz. My examples are commands, but the same things can be done with menus and/or graphical interfaces (it would just take a lot more words to describe). Possible ways to identify the residues: (a) with a simple distance cutoff (Select... Zone... or in commands) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#zones command example: color red :.a & :.b za<5 - that would color atoms in chain A that are within 5 angstroms of any atom in chain B; you can include a distance limit in many other commands, such as "select" "display" "repr sphere" "surface" etc. The "za" means atom-based cutoff, whereas "z" or "zr" means residue- based (would color whole residues with any atom within that distance). You would then use a similar command for atoms in chain B close to atoms in chain A. (b) with Find Clashes/Contacts (under Tools... Structure Analysis) or command "findclash" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html command example: findclash :.a overlap -0.5 hb 0 makePseudobonds false select true ~select ~ :.b - the first command selects any atoms outside of chain A that are close to chain A (any atoms with VDW surfaces within 0.5 angstroms of the VDW surfaces of atoms in chain A). The second command deselects atoms NOT in chain B, so what you have left are just the atoms in B that are close to A. Then you can do what you want to the selected atoms with the Actions menu or other commands (including writing out a list of the atoms or residues). Next, use similar steps to get atoms in chain A that are close to the atoms in chain B. (c) with Intersurf (under Tools... Surface/Binding Analysis) or command "intersurf" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/ intersurf.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/intersurf.html command example: intersurf :.a :.b select true prune 10 That would select all the atoms from both chains found to form the interface. See the links above for the algorithm. The "prune" distance controls how far out to the sides the interface is computed and thus how many atoms will be selected. Intersurf creates a special interface surface and opens a dialog for recoloring it based on the distances between the subunits. If you don't want that surface, you can just close it. One other thing I should mention is that sometimes "surface" (display molecular surface, which is different than the special "intersurf" surfaces) will enclose multiple chains in the same surface when instead you wanted a separate surface for each chain. You can tell Chimera to make separate surfaces, as explained here: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-February/ 002382.html 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