Hi Ann, Chimera won't move the atoms when it creates the bond, it simply adds the bond. So one issue is that the user needs to manually position one structure relative to the other before adding the bond. To move the structures separately with the mouse, you can toggle their activation status, for example using the Active checkboxes in the Model Panel (under Tools... Favorites). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> The second issue is that you can't bond atoms in different models, so after the desired relative position has been attained, combine them using the new "combine" command or "copy/combine" function in the Model Panel (you need a recent daily build for these to be available). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Then the bond can be added with the command "bond" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> or Build Structure (under Tools... Structure Editing), Add/Delete Bonds section: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 5, 2008, at 3:40 PM, Ann Spevacek wrote:

Hello - I am trying to make a bond between a protein and a polysaccharide chain in Chimera and am not quite sure how to do it. I am also curious as to whether the program will take into account interactions such as sterics when it generates the bond.

Any guidance will be greatly appreciated! Thanks, Ann Spevacek Millhauser Lab UCSC