Re: [Jmol-developers] minimization

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

Angel Herráez wrote:

>So I've being playing for a few days with the minimization of structures in Jmol, and I'm very 
>happy with the result; I think it will make an excellent educational tool. I'm feeding Jmol with 
>2D structures drawn and then exported into MOL format. 
>(All this runs within a single web page, though I'm not ready yet to go public with it.)
>
>One thing I miss, and would be interesting to have, but likely not trivial to implement, is 
>retention of the stereochemistry.
>  
>
that's next. I have an idea but no time to work on it. It would involve 
the MOL2 format bond stereochemistry designations.

>Despite being 2D, formula drawing programs allow to put wedge bonds (up/down), and at 
>least  JChemPaint exports them correctly into MOL format. However, since the Z coordinate 
>is zero for all atoms, that stereo info is lost.
>
>I can think of a way to set some positive or negative Z value on each atom depending on 
>the type of stereo bond (even using Javascript) and so modifiy the MOL before giving it to 
>Jmol, but then I'd need that Jmol retains that configuration, which it is  not doing right now 
>upon minimization.
>
>  
>
Try at least setting Z values differently for the different atoms. Are 
all the H atoms there? It will help a lot if the H atoms are on the 
carbons that might otherwise invert.

>I realize the implications for the calculation are heavy, and it may even be undesirable to 
>have it active by default --could be a toggle option--.
>
>  
>
Many others have struggled with this -- we will not solve it in a day. 
But if you can experiment with setting those Z values, if you come up 
with something relatively simple, I might be able to implement it.

Bob


>Any insights?
>
>
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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