I think this is out of my league. Rich wrote:
>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 > > ------------------------------------------------------------------------- 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
