Dear chimera support, I am a huge fan of chimera and I have so say I spend a lot of time on chimera these days, as a part of writing for my dissertation. I have a few questions and I sincerely you to request to help me out. 1. About findHbond: I never seem to get this one right. I model Enzyme-inhibitor complexes on patchdock. The inhibitor templates are either pdbs from rcsb or modelled on swissmodel. I am not able to locate or find any hbonds newly formed in the docked models, when I search for intermodel hbonds (I am looking for protein-protein interactions). Are there any special criteria or am I missing some thing? I want something similar to that of the output of HBPLUS (I never seem to get this working either - very frustrating) 2. About find clashes: What are the ideal parameters for clashes and contacts. I tried several things, they give me several no of overlaps for several different parameters. Are these vanderwaals interactions? because some times I see more than 40 interactions between two residues -i.e., between the atoms of Enzyme and inhibitor? How reliable are these interactions (I need to publish my data) This tool does not seem to work unless I add hydrogens to both the chains. 3. It would be great, if there was a energy minimization tool in chimera because I introduce mutations. Please kindly suggest me if there are any easy to use tools for this. I tried COOT and swisspdbviewer, but not really that user-friendly. I read all the newsletter e-mails from CHIMERA users-list everyday. Thanks to Elaine, tom, eric and conrad. You guys rock.. sincerely Hari hbahudha@fau.edu