Re: [Jmol-users] Atom Replacement Problem

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

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 <ot...@ch...>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 <ha...@st...> 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 <ang...@ua...>
>>
>> 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
>>
>> _______________________________________________
>> Jmol-users mailing list
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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
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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