Here is Bob Hanson's reply, from late October, to my inquiry regarding Jmol's ability to sprout hydrogens as was possible within Chime. (My knowledge is not sophisticated enough to know whether this line of pursuit might meet your needs, but here it is.) There was little feedback from others so I believe it was dropped or back-burnered. Byrne
> 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 On 1/29/07 3:16 PM, "Francesco Pietra" <[EMAIL PROTECTED]> wrote: > Let me say that a package dealing with molecules that > does not place hydrogens correctly is of no use > professionally. I must add that I am strongly > disappointed, and back to my old MM package, which > places the hydrogens correctly, like the nonvolatiles. > How do you start a quantum mechanical computation with > hydrogens not at their due place? > Cheers > francesco pietra > > > --- Angel Herraez <[EMAIL PROTECTED]> wrote: > >> I am opening two new threads for Paul questions in >> his last post to " >> loading jmol file from open babel" >> >> On 29 Jan 2007 at 10:44, H. Paul Benton wrote: >>> To all the other uses I have one more question to >> ask >>> "If a file was loaded with no Hydrogens how can I >> get >>> Jmol to put them on?". >> >> Jmol cannot add hydrogens right now. Remebre it is a >> viewer, not a molecule builder. >> I can recommend two programs that allow you to do >> so. One is Discovery Studio Visualizer, >> from Accelrys (formerly known by several names such >> as WebLab Viewer, Accelrys Viewer, >> DS Viewer, etc.) >> The other is ChemSketch, from ACDLabs. This is >> actually a 2D chemical drawing package, >> but imports and exports MOL files and has a 3D >> module. >> >> If you haven't used any of them, go for DS >> Visualizer. It will open your pdb, mol, xyz etc >> files, >> then go to menu Tools > Hydrgens > Add and save >> again. >> >> >> >> >> > ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get >> the chance to share your >> opinions on IT & business topics through brief >> surveys - and earn cash >> > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > > ______________________________________________________________________________ > ______ > Want to start your own business? > Learn how on Yahoo! Small Business. > http://smallbusiness.yahoo.com/r-index > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
