How do you decide on how pyramidal (or not) to make a N Bob? What about hydroxyl H atoms when there is the potential for intramolecular H-bonding?
Rich On Fri, 15 Jan 2010 11:01:22 -0600, Robert Hanson <[email protected]> wrote: > OK, that's in. See Jmol 11.9.19 --- > http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip > > calculate hydrogen # adds the hydrogen atoms to C,N,O,and S atoms, > respecting bonding but not considering formal charge (for now). > > minimize addHydrogens # minimizes and then adds H atoms at the end > > delete {hydrogen} # does that > > Bob > > On Thu, Jan 14, 2010 at 9:14 PM, Grossman, Robert B > <[email protected] >> wrote: > >> My suggestion would be that if a multiple bond is not specified, you >> should >> assume a single bond, and if a charge or radical is not specified, you >> should assume enough H atoms to give the atom its octet. If the user is >> not >> specifying multiple bonds, then he simply shouldn't use the function. >> >> Consider the MOL file below. Some H atoms are specified, some not. I >> had >> Jmol do a minimization, and it correctly deplanarized the isopropyl >> group. >> If it can do that, then it can easily position the H atoms. ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
