Re: [Jmol-users] Aromatic bond rendering

[Bob H. <ha...@st...>]

Well, guess what? I think I figured it out.

version=11.3.29 (Nico -- this is ready for release)

# new feature: aromaticSingle and aromaticDouble bond order options
# new feature: select ISAROMATIC     # selects aromatic atoms

bonds that look like single and double bonds can still be considered 
aromatic, and atoms connected by such bonds can be selected using 
ISAROMATIC. (AROMATIC itself is a RasMol reserved keyword).

# new feature: "smartaromatic" bonds # turned off with "smartAromatic = 
false"
# new feature: calculate aromatic    # calculates reasonable aromatic 
double/single alternation.  
# new feature: reset aromatic        # sets all aromaticDouble and 
aromaticSingle back to aromatic

Jmol will now calculate alternating aromatic bonds. This should go a 
long way to improving the look of aromatic rings. You can turn this 
feature off using

  smartAromatic = false

And you can specify the alternation by indicating any one bond's state 
and then recalculating

reset aromatic
connect (atomno=9) (atomno=12) aromaticDouble
calculate aromatic

# new feature: MOL reader recognizes bond types 4,6,7

4 is loaded as aromatic
6 and 7 are loaded as aromaticSingle and aromaticDouble

Bob

Angel Herraez wrote:

>El 4 Oct 2007 a las 7:41, Bob Hanson escribió:
>  
>
>>I'll look into this. But it is a VERY difficult problem, actually.
>>    
>>
>
>In fact, I thought it was impossible, and had given up on it until 
>Bob posted yesterday about negative signs.
>
>I agree with Rolf, but the "inner" location is only clear with single 
>rings. Take for ex. purine and you are bound to have trouible 
>deciding which is the inner side of the shared bond. Not to mention 
>more complex polycyclic molecules!
>
>  
>
I looked at the algorithm. It's very simplistic -- find the

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-- 
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