whenever the popup window is different, it means the state is not being saved correcly.
Nick Greeves wrote: > Thanks Bob that works nicely and it even does C=O. > > However there is a problem with the popup window feature. It shows the > version with every bond aromatic rather than the desired version with > only double bonds. This can be fixed by "calculate aromatic" on the > new window but it spoils the effect of the popup window. > > I found that connect aromatic auto seems better in that regard. The > popup window is now fine > > Any ideas why these two behave differently with the popup window and, > is there a downside to using connect aromatic auto? > > All the best > > Nick > > -- > > 3D Organic Animations http://www.chemtube3d.com > > Tel: +44 (0)151-794-3506 (3500 secretary) > > > > > On 3 Apr 2008, at 07:43, [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> wrote: > >> Date: Wed, 02 Apr 2008 23:00:10 -0500 >> From: Bob Hanson <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> >> Subject: Re: [Jmol-users] Automatic generation of multiple bond types >> To: [email protected] >> <mailto:[email protected]> >> Message-ID: <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Nick Greeves wrote: >> >>> Is there a command which will generate multiple bond types (even just >> >>> double would be a start) from a structure that lacks such info e.g. >> >>> .xyz ? >> >>> >> It's >> >> select {*} // maybe >> connect aromatic modify >> calculate aromatic >> >> The idea is that aromatic systems are conjugated systems, and Jmol knows >> how to follow the conjugated single/double sets in a clever way to >> always produce the best set of double bonds (if there is one). >> >> You can actually select all the atoms, but I don't recommend it, because >> that might throw off minimization. What I was doing for caffeine was: >> >> select connected(2) or connected(3) or oxygen and connected(1) >> >> At least that was good enough for caffeine. A general solution would be >> somewhat more specific -- connected(3) and (not nitrogen or nitrogen and >> connected({oxygen})) -- something like that. You want to include the >> carbonyls even though they are not technically aromatic. >> >> Bob >> > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services for >just about anything Open Source. >http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
