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On Feb 7, 2010, at 11:13 PM, Wataru Kagawa wrote: > Hi all, > > I would like to create a pdb file for a chemical compound (FW ~600) that was created in our chemistry department. ChemDraw 3D appears capable of doing this, but I would like to know if there are free alternatives that work great on Macs. Any info would be greatly appreciated. > > Thanks. > > Wataru Hi Wataru-san: Three easy steps: 1. Define a SMILES string for your compound. The java molecular editor makes this easy: http://www.molinspiration.com/jme/ 2. Paste the smiles string into COOT, or feed it into phenix.elbow 3. Output the pdb file. COOT is faster but phenix.elbow allows you to minimize the structure, even using third-party QM programs like GAMESS. I trust all is well. Bill