I am looking for references to algorithms on detection of hydrogen bonds. Web references or electronic copies of documents are best since I do not have access to a library.
Thanks Miguel More Detail ----------- I need to implement the RasMol commands hbonds <boolean> set hbonds backbone | sidechain As I understand it, the general algorithm is to look for O & N atoms that are within some distance. To get started, I need some very basic background on this. Like, introductory undergraduate stuff. I have done a little searching on the web and found the following. It seems related to Deep View / Swiss PDB Viewer. The document says that it is a draft, but it seems valuable to me: http://matterhorn.niehs.nih.gov/draft1/draft16.html Properties of the H-bond detection routine: H-bonds are computed only between different groups. Intramolecular H-bonds are not detected, but can be built manually. H-bonds are detected on the basis of distance, atom type (as defined in ref.[1]) and angle. When an atom passes H-bond criterion for several other atoms, all possible H-bonds are drawn. There is no attempt to choose the best one. Default limits are a distance of 2.2 to 3.3 � (or 1.2 to 2.76 � when hydrogens are present) and a donor-H-acceptor angle of 90� (120� with hydrogens). Default margins for including weaker bonds are 0.05 �. HETATM atom types are not defined, so Deep View must make assumptions about atom types, and can guess wrong about donor/acceptor properties. For example, N is assumed to be an H-bond donor, but this is not always true. As a result, some impossible H-bonds can be drawn from or to hetero atoms. ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
