Hi Junwei, FindHBond (and command "findhbond" or "hbonds") uses detailed criteria that depend on the atom types. There isn't just one distance or angle, but different ones for different combinations of donor and acceptor types. As mentioned here, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ findhbond.html#criteria the cutoffs are from a paper based on very-high-resolution small molecule crystal structures: J.E.J. Mills and P.M. Dean, "Three-dimensional hydrogen-bond geometry and probability information from a crystal survey" J Comput-Aided Mol Des 10: 607 (1996). The cutoffs are in Tables 5-8. Depending on the atom types, there may be two or three angle criteria, and donor-acceptor distance criteria are mostly near 3.0-3.4, although they range from 2.87 (protonated carboxylic acid donor) to 3.73 (thiocarbonyl acceptor). In addition, because structures in the PDB are generally lower resolution than those small molecules, the values from the paper are relaxed by 0.4 angstroms and 20 degrees (by default; you can change those amounts). Best, 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 Mar 28, 2008, at 1:17 AM, zhaojunwei wrote:
Hi, all I have a question about the hbond. What is the definition about hydrogen bond in chimera? As we know, there're different criterias among softwares, I'm wondering the distence between donor atom and acceptor atom, and the angle of donor-hydrogen-acceptor in chimera.
Any reply will be deeply appreciated! It'll be kind if you can send the reply to my address, cause I'm not in the mailing list.
Junwei Zhao