Dear Fabian, You can add the final bond with the "Build Structure" tool (under Tools... Structure Editing) or the command "bond": http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm... http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html You may want to rotate torsions to get the ends closer together before adding the bond: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc... You may already know about the "Minimize Structure" tool and "minimize" command. You can allow only parts of the structure to move during minimization. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.h... http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html However, this process will not likely generate a high-quality model, as minimization only goes so far in removing strain and will not cross barriers to find more likely conformations. It may suffice if you are aware (and don't mind) that it is a rough model, or you may use the structure as a starting point for MD or MC simulations with another program. Alternatively, you could look into other approaches to building the linker. A few programs that might do that are Modeller, MolIDE, RAPPER: http://salilab.org/modeller/index.html http://dunbrack.fccc.edu/molide/molide.php http://mordred.bioc.cam.ac.uk/~rapper/ (I haven't tried to use any of these for de novo loop building, however). I should also mention that "addaa", unlike "swapaa", currently doesn't use rotamer libraries, so it may not give the best sidechain conformations. There is a little more discussion about Chimera and protein modeling in this post: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-January/002202.html Best, 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 May 18, 2008, at 4:20 AM, Fabian Gmail wrote:

Dear Chimera experts, I am willing to build a peptide "linker" connecting two different pdb chains, that is to connect two existing pdb chains with a new peptide chain, and if possible minimize it. Is it possible to do that wich chimera? I know the command addaa, but to my best understanding this command it's not able to connect the end of the new peptide with the beginning of the second chain.

Any suggestions will be greatly appreciated. Best regards and thanks a lot in advance, Fabian