Hi Fabian, Chimera tries to figure out what the "main" molecule is; by default, the surface encloses that set of atoms. You can tell it to instead enclose different sets of atoms (in this case, your chains) with the command "surfcat". Example: 4hvp is HIV protease, made of chains A and B. By default, "main" is identified as including both A and B, so the surface encloses the whole thing, except the ligand. You can see that with the commands: open 4hvp (open the structure) rainbow chain (give chains different colors to make the issue clearer) surf (show surface for "main" - see there is just one surface around both chains) ~surf (hide surface) (That stuff could also be done with the menus, but it would take more words to describe) To instead make separate surfaces for chain A and chain B, use the commands: surfcat part1 :.a surfcat part2 :.b surf part1 surf part2 "part1" and "part2" are just names, you could use different ones. 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 P.S. more info on how the default set "main" is identified: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html and manual page for surfcat: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html On Feb 29, 2008, at 12:04 AM, Fabian Gmail wrote:

Hi all, I enjoy very much using chimera, I have a question regarding surfaces. When I am working on a multi chain protein complex, and I want to present only one chain as surface and the others as ribbon or sticks, oftenly the surface present "holes" on the contact points with the ribbon. I understand they represent contact points between the chains, but I don't like how the surface looks like. Is there a way to avoid this? (I do that but uploading another copy of the chain). Thanks a lot, Fabian -- Fabian Glaser, PhD

Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL

Web: http://bku.technion.ac.il Email: fglaser@tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396