Hello all, I saw a couple of posts on this from a year ago but didn't find a conclusive answer to how to tell phenix to insert a covalent bond between a cysteine residue and a bound inhibitor. I have the inhibitor (a small molecule) modeled in but haven't figured out how to insert the covalent bond. I used PRODRG to generate the inhibitor pdb and eLBOW to generate a cif file. The distance between the sulfur on the cysteine and the first carbon atom in the inhibitor is 1.8A. Do I need to run eLBOW using the protein-inhibitor pdb to generate an appropriate cif file? I see in phenix.refine under the PDB interpretation tab their is a box for "add link to CIF"....is this where I need to tell phenix to insert the covalent bond? I guess I could just draw the inhibitor-cysteine complex as a modified amino acid and try inserting it that way..... charles -- Charles Stewart Jr., PhD Research Associate Chemical Biology and Proteomics Laboratory-Noel Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 Phone: (858) 453-4100 x1946 Fax: (858) 597-0855 Email: [email protected]