Hi Farhana, You can open several different structures from different files and display them all in the same window. It sounds like you figured that part out already. Then you can freeze/freeze structures (we call that "activation" and "deactivation" for motion) so that only the active ones can be moved with the mouse. Activation/deactivation can be controlled in several ways: - checkboxes under the Command Line (show with Favorites... Command Line) - Model Panel (Favorites... Model Panel), checkboxes in the Active column and/or various "activate" function buttons on the right - with the "select" command See <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef

Or if you are moving structures with commands, in newer versions of Chimera (1.4, so daily builds), you can specify which models you want to move. Movement commands include "move" (translation) and "turn" (rotation). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> 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 http://www.cgl.ucsf.edu/home/meng/index.html On Aug 6, 2009, at 11:08 AM, Farhana F Syed wrote:

Hello,

I recently downloaded chimera and have been using to view my protein homology model - mainly to show the 2 residues that could be involved in binding to a molecule inside the cell. For that purpose, I need to be able to open the small molecule (citrate or phosphate) in the same window with protein; so I can show the small molecule binds to the specific amino acid residues. But even if I open the two together, how do I pick the small molecule and move it around where I need it?

Please help. Thanks, Farhana