On 10-9-2006 9:54, Bob Hanson wrote: > Side-chain hydrogen bonds: > --------------------------- > I'm not presently working on this. One of the major issues there is > sprouting the hydrogens and getting the hybridization right for both > proteins and nonproteins. Also an issue is the rotational freedom around > the C-O-H bond of alcohols and phenols. Is there a general solution to this? >
No. In the vast majority of crystal structures (and all protein structures) the H atoms are guessed at. In most small molecule structures you only have information on the heavy-atom positions and in most protein structures you don't even have that (because of all the restraints required for sensible refinements). At least for proteins you can guess correctly the hybridization almost always just based on the identity of the residue but when you are trying to do the small molecules (either on their on or when included as ligands in macromolecular structures) the problem becomes much larger. Getting it mostly right for small molecules requires a pretty extensive analysis of, first the molecular structure and, second, its inter- and intra- interactions. This last is the only way to come up with a guess for -OH positions (and, rarely, NH positions) because you need to look at all potential acceptor and donor heavy atoms and rank their importance. Rich ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
