hint: see http://chemapps.stolaf.edu/quaternions/jmol/helix.htm
On Fri, Feb 12, 2010 at 9:25 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> Have a methyl radical precalculated as data. Merge it; translate/rotate it
> to align it. Add the bond. A good challenge.
>
>
> On Fri, Feb 12, 2010 at 1:06 PM, Otis Rothenberger <o...@chemagic.com>wrote:
>
>> 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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
>>> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
>>> http://p.sf.net/sfu/solaris-dev2dev
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>>>
>>
>>
>> --
>> Otis Rothenberger
>> http://chemagic.org
>>
>>
>> ------------------------------------------------------------------------------
>> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
>> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
>> http://p.sf.net/sfu/solaris-dev2dev
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>> Jmol-users@lists.sourceforge.net
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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
>
--
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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