Bob, Thanks for looking into this. I am not a sophisticated user so I can;t comment on 4, 5, & 6. I mostly am making tutorials for my AP Biology students which also are used by other teachers for general Biology students at the high school level. That said, here's what would work for me.
I've only used PBD models. I'm trying to emphasize the fit between substrate and active site as well as hydrogen bonding. So it would be nice to extend the sprouted hydrogen set from carbons to at least include those involved in hbonding. The ideal would also include hydrogens involved between residues in the specificity pocket and those on the non-residue substrate. I extensively searched the archives and found no mention of sprouted hydrogens. If I the only one asking, please don't go out of your way on this. Thanks, Byrne On 10/26/06 7:24 AM, "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> wrote: > I've been looking into sprouting hydrogens, and it's no problem. The only > thing is what do people really want. Please start discussing what you > want. > > 1) Only PDB models (like Chime)? > > 2) Only the 20 common amino acids (like Chime)? > > 3) Just carbons or all atoms? > > 4) If not just PDB residues, suggestions for resolving oxidation state > ambiguities like -CCCO, which could be CH2CH2CH2OH or several other > possibilities. > > 5) If not just carbons, suggestions for resolving pKa issues. > > 6) If not just carbons, suggestions for resolving dihedral selection. > > 7) full model or selected subsets? > > > Bob > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
