From: Robert H. <ha...@st...> - 2008-11-05 18:56:09
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OK, that's uploaded. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm and http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip On Wed, Nov 5, 2008 at 8:59 AM, Robert Hanson <ha...@st...> wrote: > oops -- that didn't work -- will have this corrected later this morning. > Looks like 90 degrees is more reasonable -- 120 cuts out way too many. > > > On Tue, Nov 4, 2008 at 8:25 PM, Robert Hanson <ha...@st...> wrote: > >> 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 >> > > > > -- > 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 |