From: Robert H. <ha...@st...> - 2008-11-05 02:25:11
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should be adjustable -- but I haven't actually tested it. Just thought I would get that out there for inspection. David -- to a first approximation, of course, if you have the H atoms and you can live with just distance and a parameter, it's just a connect command to produce all those hydrogen bonds. If you need more, then it's just a matter of defining what angle requirements one might want. Bob On Tue, Nov 4, 2008 at 7:49 PM, Thomas Stout <tho...@gm...> wrote: > > It looks nice! -- is the angle adjustable? I tried setting it to other > values (even extreme values) and didn't see any change in the created H > bonds.... > > -Tom > > On Tue, Nov 4, 2008 at 4:40 PM, Robert Hanson <ha...@st...> wrote: > >> see >> >> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm >> >> The min/max distances are same as for other H bonds: >> >> hbondMax = 3.25f; >> hbondMin = 2.5f; >> >> These values aren't currently adjustable. >> >> comments requested >> >> >> >> On Tue, Nov 4, 2008 at 5:23 PM, Robert Hanson <ha...@st...> wrote: >> >>> Possibly. Is that documented or discussed somewhere in the literature? >>> >>> I could probably implement that tonight while watching the election >>> returns then let you try it out. I propose: >>> >>> calculate hbonds {atomset1} {atomset2} >>> >>> maybe with some settings for minimum and maximum distances. >>> >>> Bob >>> >>> >>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> 1520 St. Olaf Ave. >>> Northfield, MN 55057 >>> http://www.stolaf.edu/people/hansonr >>> phone: 507-786-3107 >>> >>> >>> If nature does not answer first what we want, >>> it is better to take what answer we get. >>> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>> >> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |