Bob and Angel-
Thanks for the help and the words of encouragement. My objective is to
create the Jmol equivalent of an old Prentice Hall Model Kit, and a
molecular builder (editor, I guess) is part of this objective.
At present, I only know how to build molecules in Jmol using univalent atoms
as a spring board via replacement. I have users start with methane, ethene,
ethyne, or methanal. They can then click/change any univalent atom to C, H,
O, X, or N. Your newly added minimize does the rest. I said it before, and
I'll say it again: for folks interested in small molecules, this was a super
addition to Jmol.
I'd love to build C directly onto C (i.e. actually add a C, O, N etc.), but
I'm not sure how to proceed. If you can point me on this, I'd appreciate it.
The clean up at the end of my current routine is really not bad visually. I
had to do it to keep the growing molecule in the window, especially when
"adding" methyl groups:
http://chemagic.com/web_molecules/script_page_large.aspx
Other Points:
1) atomno's are duplicated during this building process (i.e. during the
addHydrogens step). That's why I used atomIndex.
2) Holding addHydrogens until the end of several changes fixes the bond
length issue. Unfortunately, it also eliminates the hydrogens as sequential
handles for further chain growth.
3) Question: Is there a way to strip H's and then add them back in?
Otis
On Fri, Feb 12, 2010 at 6:30 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> valency accounts for bond order. So just about every carbon will be
> tetravalent, regardless of is position in a molecule -- acetylene, ethene,
> ethane all have {_C}.valence = 4. But if there are only three single bonds
> to a carbon, its valence will be reported as 3.
>
> By the way, Otis -- you will have more bugs to report. No one has done much
> with this, and I think you are going to find more places where Jmol doesn't
> do what you expect it to do. Just keep reporting these.
>
> Bob
>
> 2010/2/12 Angel Herráez <angel.herr...@uah.es>
>
> Sorry, Otis, I cannot help with your problem (but the feature looks
>> exciting! One more step towards a Jmol editor, even if a simple one.)
>>
>> Your post prompts a question: is this "valency" property a shortcut
>> meaning "number of bonds"? Bob?
>>
>>
>>
>>
>>
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>
>
>
> --
> 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
>
>
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--
Otis Rothenberger
http://chemagic.org
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