If you send me the PDB file, I will take a look. But because you are defining the CONECT records, Jmol will respect that and not automatically connect Ser 200 to the inhibitor (which is probably a HETATM, right?) Try
set forceAutobond TRUE prior to the load commmand and see if that does the trick. > Hi All, > > I am making a tutorial to illustrate the mechanism of enzyme catalysis of > hydrolysis of an ester. The PDB file that I am using shows the Ser 200 at > the active site covalently bonded to an inhibitor which is bound at the > active site, and does not contain any hydrogen atoms. I added two hydrogen > atoms to the file, one was identified as a Ser 200 atom and the other one > as > a His (also at the catalytic site) atom. Both atoms were displayed at > appropriate locations. My problem is that the Ser is no longer bonded to > the inhibitor, even though the Conect commands are still in the PDB file, > and using the Jmol connect command I can show the Ser bonded to the > inhibitor at the appropriate place in the mechanism. I use the connect > command to make, delete or change the nature of other bonds associated > with > the active site. I do not understand how the information in a PDB file is > used to make the covalent bonds well enough to know how I affected the Ser > bonding by adding the hydrogens. Any suggestions would be greatly > appreciated. > > Karl > > > > Karl M. Oberholser, Ph.D. Phone: > Professor of Chemistry Voice: 717-766-0512 > Chemistry & Biochemistry Dept. Fax: 717-691-6046 > Messiah College e-mail: [EMAIL PROTECTED] > P.O. Box 3049 > One College Avenue > Grantham, Pa 17027 > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace_______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
