Hi Jeffrey, You can definitely control this, there are a couple of ways. By default, a model gets divided up into categories named solvent, ions, ligand, and main. What you are seeing is the "main" surface that includes both protein and DNA. <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html> One way is to use the "split" command to put each chain in a separate model. <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html> The other way is to use "surfcat" to create your own categories with the desired content, then "surface" to show the molecular surface of the category. <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html> For example, commands: ~surf surfcat myprot protein surfcat mydna nucleic acid surf myprot surf mydna The commands take any kind of command-line specification, not just "protein" and "nucleic acid" like above. For example, surfcat achain :.a (all of chain A) surfcat achain :.a & ~ solvent (all of chain A except solvent) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 24, 2011, at 11:47 AM, Jeffrey Kentner wrote:
Hello, I am trying to create a nice aesthetic model of a protein binding to DNA. When I show molecular surface, the program doesn't seem to be able to differentiate between the DNA chain and the protein chain. I either end up with a surface on the DNA which is not fully closed, or if I extend the surface via the 'surface zone' it simply begins to cover the protein as well... I have consulted the documentation and can not find any description of how one would isolate the molecular surface to a particular chain. Is this not possible in Chimera? Cheerio, Jeffrey