Dear Sriram, Chimera does not do docking -- it does not predict how structures will bind each other. For docking calculations, you would need to get another program such as DOCK: <http://dock.compbio.ucsf.edu/> Alternatively, you could try to dock the structures by hand in Chimera (move them relative to each other and rotate bonds), but it is generally difficult. However, Chimera includes (a) a Dock Prep tool for preparing structures before docking (b) a ViewDock tool for looking at the output from DOCK, and an associated tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> Besides the docking calculation, you have another problem -- you need a 3D structure for your compound. If it is something that you can find in PubChem <http://pubchem.ncbi.nlm.nih.gov/> you may be to use "File... Fetch by ID", choose "PubChem" and then enter the compound's CID number to get a 3D structure. This uses a web service provided by Chembiogrid at Indiana University. For example, I went to PubChem and searched for "diphenhydramine." I see it has the CID 3100, which allows me to fetch the 3D structure into Chimera. 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 Jan 4, 2010, at 12:40 PM, SRIRAM SATAGOPAN wrote:

Hello,

I have a receptor molecule (pdb file of the protein) and the chemical formula for the compound that I want to dock it with. I am assuming that I need to use the viewdock program to look at the docking interactions, but I just don't know how to go about it without a structure file for the ligand molecule. Is there a simple way to generate the coordinates for the ligand from the chemical formula? I would appreciate if someone in the group can help me out with this.

Thanks. Sriram