Otis -- I think you are very close to having a full-fledged molecular editor
up and running with Jmol. Great to see that.
On Tue, Mar 23, 2010 at 7:12 PM, Otis Rothenberger <[email protected]>wrote:
> Bob,
>
> Your first suggestion cleared up my atomIndex problem. You explained {*}[0]
> to me once before, and it did not sink in. Now I see that it's exactly what
> needed. It's atomno = max. Is that correct?
>
right
>
> Your second suggestion is really slick, and I learned a lot picking it
> apart. Unfortunately, it leads to linear chain growth from time to time, and
> that starts getting into problems. Ethane growth seems to be linear
> consistently - i.e. C-C-C. If you build off of C2, you start to add
> superimposed atoms, as per your Jmol math.
>
> Right -- you could check for that and do something different then.
> The _atomPick X+0, Y+.1, Z+.1 that I used seems to do two things: 1) the
> atoms are close enough to bond; 2) the atoms are offset enough for minimize
> to push the new atom away.
>
>
I just thought it was very odd to have the groups already present invert
chirality completely.
> The atom substitution approach is the best way to grow the chain, but I
> wanted to have an addition option to mimic standard drawing programs. Your
> original suggestion clears up my problem.
>
> Question: Is double click measure a possibility here? Specifically, are the
> positions of double click 1 and double click 2 stored for use so that the
> new atom could be plopped at double click 2 position (on background)? I
> don't use Spartan, but that approach to addition would just about match Chem
> Office Chem3d.
>
>
not stored.
> Otis
>
>
>
>
> On Tue, Mar 23, 2010 at 7:53 AM, Robert Hanson <[email protected]> wrote:
>
>> Right, that makes sense. When you delete atoms, Jmol does not actually
>> remove them. It just marks them as "deleted". This is to save time and lower
>> the chance of all sorts of problems later. So your value for "i" will be
>> off. You need this:
>>
>> select atomIndex=_atomPicked;
>> flash
>>
>> var x = {atomIndex=_atomPicked}.atomX;
>> var y = {atomIndex=_atomPicked}.atomY+.1;
>> var z = {atomIndex=_atomPicked}.atomZ+.1;
>> set appendNew false;
>> var w = '1\ntest\nC ' + x + ' ' + y + ' ' + z + '\n';
>> print "A " + {*}.length + " " + _atomPicked
>> data 'append @w';
>> print "B " + {*}.length + " " + _atomPicked + {atomIndex=_atomPicked}
>> var i = {*}[0].atomIndex
>>
>> connect (atomIndex=_atomPicked) (atomIndex=i) single;
>>
>> You might consider a different way to add that atom position:
>>
>> var a = {atomIndex=_atomPicked};
>> select a
>> flash
>> var pt = a.xyz * 2 - {connected(a)}.xyz
>> set appendNew false;
>> var w = '1\ntest\nC ' + pt.x + ' ' + pt.y + ' ' + pt.z + '\n';
>> data 'append @w';
>> var b = {*}[0]
>> connect @a @b single;
>>
>>
>> On Mon, Mar 22, 2010 at 11:29 PM, Otis Rothenberger <[email protected]>wrote:
>>
>>> Bob,
>>>
>>> I am having an atom index problem building a carbon chain. I set the
>>> stage for this with the following script:
>>>
>>> delete hydrogens;echo Clicked atoms will|ADD a carbon atom.;
>>>
>>> If at this point I check atomIndexes, and they are A-OK. The hydrogens
>>> are gone, and the atomIndexes run from 0 to the new number of atoms -1.
>>>
>>> The carbon atom click/add then uses the following script:
>>>
>>> select atomIndex=_atomPicked;flash;var i = {*}.atomIndex.max + 1;var j =
>>> i + 1;var x = {atomIndex=_atomPicked}.atomX;var y =
>>> {atomIndex=_atomPicked}.atomY+.1;var z =
>>> {atomIndex=_atomPicked}.atomZ+.1;set appendNew false;var w = '1\ntest\nC ' +
>>> x + ' ' + y + ' ' + z + '\n';data 'append @w';connect
>>> (atomIndex=_atomPicked) (atomIndex=i) single;
>>>
>>> Flash is my own command that simply substitutes the Jmol script to flash
>>> the atom magenta for .5 seconds prior to jmolScript()
>>>
>>> If I do NOT delete the hydrogens (step 1 above), then the script works
>>> nicely. If I do delete the hydrogens (step 1 again) the first click/add
>>> fails to bond -
>>>
>>> i.e. connect (atomIndex=_atomPicked) (atomIndex=i) single
>>>
>>> is failing. The new carbon atom is added, but it floats away without
>>> connecting on a subsequent minimize. After this first failure, the script
>>> works on subsequent clicks.
>>>
>>> I could simply leave the hydrogens on, but I'm trying to give the editor
>>> the feel of standard editors that build C frameworks.
>>>
>>> The working page is here:
>>>
>>> http://chemagic.com/web_molecules/script_page_large.aspx
>>>
>>> Click Display Control Panel.
>>>
>>> The page is set to do the with-hydrogen edit (works). If you do a delete
>>> hydrogens in the text command field, you will see the problem on the first C
>>> add.
>>>
>>> Any thoughts on the problem? It appears for the first click atomIndex=i
>>> is not what I think it is??
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> http://chemagic.org
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Download Intel® Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev
>>> _______________________________________________
>>> Jmol-users mailing list
>>> [email protected]
>>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>>
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> 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
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
