Hi Peter, AddH (GUI or command) with the "consider H-bonds" option turned on does place hydrogens to fulfill hydrogen bonds for water as well as the protein, but it does not explore all the possible hydrogen- bonding network configurations to find some type of global optimum. Actually, I do not know if any method guarantees a global optimum, but various programs use different heuristics to narrow the search space. We do suggest one alternative, somewhat more intensive method: Reduce from the Richardson lab. There is a link to this program and more information in the AddH man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html You might want to try both approaches on a couple of test cases to decide what to use in your project, or delve into the literature to find additional programs. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu 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 Sep 10, 2008, at 2:22 PM, P. Law wrote:

Hi, I am analyzing water-water and water-protein hydrogen bonds in a dataset of high resolution crystal structures. As part of this analysis, I will need to add hydrogens to water molecules and to the protein. I was wondering how well the "addh" tool can place hydrogens on water molecules in the first shell around the protein? If addh is not the right tool for this task, are you aware of any freely available programs that can add hydrogens to 1st shell water molecules in PDB files? Thanks for your help!

Sincerely, Peter Law Graduate Student Biochemistry Department University of Washington