Hi Joseph, Chimera does not do automated docking, but you can position the structures manually. Normally you would open the protein and ligand from two separate files. Then in the Model Panel (in Favorites menu), there will be a line for each file. You can check/uncheck the "Active" box to control which are movable with the mouse. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef Several other tools may be useful during this process: FindHBond, Find Clashes/Contacts, Distances (under Tools... Structure Analysis), Rotamers, Adjust Torsions (under Tools... Structure Editing). http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc... Once you have the ligand positioned how you want it relative to the protein, you can save PDB. You can save two separate PDB files or both structures in one PDB file. If you didn't change the structure of the protein part (for example, by rotating bonds), you could save a file of just the ligand as long as you save it "relative" to the protein structure. Then, later opening the original protein file and that new ligand file regenerates your docking. It doesn't matter which file-saving approach you take, if you will be using the file(s) later in Chimera. If you intend to use the PDB file(s) as input to another program, however, it all depends on what that other program expects and you may need to do some manual editing. If you are starting with both in one file and the Model Panel only shows one line, you would need to get the protein and ligand on separate lines to allow separate motion. You could do that by text- editing to create to files, or by simply opening that file twice and then (in Chimera) deleting the ligand part of one copy and deleting the protein part of the other. For automated docking rather than doing it yourself, you would have to use a separate program such as DOCK. Then you can view the output in Chimera. 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 On Apr 3, 2008, at 7:58 AM, Boyle, Joseph J wrote:
Hello, Is it possible to use Chimera to dock a small ligand into a binding pocket pdb - and if so how is the ligand imported into the protein pdb file ? Yours Sincerely, Joseph Boyle