On Mon, Feb 15, 2010 at 11:25 AM, Otis Rothenberger <[email protected]>wrote:
> Bob,
>
> Your changes seem to address my problems nicely. I do have some timing
> issues, within Jmol Scrip and JavaScript. I need top work on these. Here is
> the JavaScript that I'm using for atom replacement following your
> modifications on the applet:
>
>
> evalRasmol("{atomIndex=" + atomIndex + "}.element = '" + buildAtom
> + "';");
>
> evalRasmol("set useMinimizationThread false;echo working...;delete
> hydrogens;minimize addHydrogens;wireframe 0.15; spacefill 23%;boundbox
> {*};centerat boundbox;minimize steps 100;");
>
> setTimeout("doUFF()",2000)
>
> The above modification of my code is pretty much the result of trial and
> error. I'm not sure I understand why, but the code must be just so. I cannot
> simply do a longer minimize in the second evalRasmol function. Further, even
> though the minimize is the last command, the "set useMinimizationThread
> false" is required.
...or what happens?
> Finally, I must call another "minimize" and it cannot follow the first
> minimize in the Jmol code string even with a delay. I must call it with a
> JavaScript timeout. The evalRasmol function is not anything sophisticated.
> It's basically a call to "appObj.script(scpt)" where appObj is the Jmol
> applet and scpt is the script string.
>
Preferably, use Jmol.js and
jmolScript()
bu this amounts to the same thing. Your naming this function "...Eval" is
probably a poor choice. There is also
jmolEvaluate()
which does an immediate evaluation of an expression and returns the value.
>
>
Nevertheless, it works with your applet modifications. Some specific points:
>
> 1) Formaldehyde to imine via N substitution for O still produces the
> strange H insertion, but the above code corrects this.
>
not sure which code you are referring to -- mine or yours.
> 2) The "delete hydrogens;minimize addHydrogens" sequence works fine with
> terminal alkenes.
>
good
> 3) I have a point and click single, double, and triple bond insertion
> routine now, and you can build ketene with this from methane. There are,
> indeed, superimposed hydrogens. If, however, I build ketene from a starting
> ethene, then all is OK. The geometry following minimize is pushing in the
> right direction, but it never quite gets there. C=C=C is a bit bent, but the
> hydrogens are moving to the correct out of plane geometry.
>
>
We may be out of luck on the minimization of cumulenes. I didn't invent the
UFF force field, and those who did probably did not consider cumulenes.
> None of this is on the chemagic server yet. I'm going to work on timing
> problems, and put it up later today, hopefully with a more intuitive
> interface. I also need to look into "delete hydrogens" at the site of change
> only. I have a feeling this will improve performance. I think the atom
> expression for these hydrogens should be easy to construct from the
> atomIndex numbers that are part of the substitution.
>
> yes I think so. you can also minimize specific groups rather than the whole
molecule.
> Otis
>
>
>
> On Mon, Feb 15, 2010 at 8:33 AM, Robert Hanson <[email protected]> wrote:
>
>> Otis, give this next one a try.
>>
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
>>
>> Basically, the atom deletion business was never fully worked out. This is
>> great help to have you testing it. I didn't check imines, just ethylene and
>> terminal alkenes. Most likely does not work with cumulenes.
>>
>> Bob
>>
>>
>>
>> On Sun, Feb 14, 2010 at 2:56 PM, Otis Rothenberger <[email protected]>wrote:
>>
>>> Bob,
>>>
>>> I think I have the latest version of 11.9.30_dev on the chemagic server:
>>>
>>> http://chemagic.com/web_molecules/script_page_large.aspx
>>>
>>> User instructions are sparse right now, but I think you can reconstruct
>>> some of my specific issues with the following brief instructions:
>>>
>>> Use the "Model Building and Other Tools" link to bring up the menu.
>>> Basically, users can pick a base start molecule (CH4, H2CCH2, HCCH, and
>>> H2CO) and select a click/replace atom for model click/replace. The basic
>>> JavaScript code for click replace is:
>>>
>>>
>>> evalRasmol("{atomIndex=" + atomIndex + "}.element = '" +
>>> buildAtom + "';");
>>> evalRasmol("minimize addHydrogens;wireframe 0.15; spacefill
>>> 23%;boundbox {*};centerat boundbox;");
>>>
>>> For testing purposes, I've put the Rectify Hydrogen as a separate link.
>>> The JavaScript code here is:
>>>
>>> evalRasmol("select *;delete hydrogens;minimize addHydrogens;");
>>>
>>> Some problem examples (Note I have not yet tried to localize delete
>>> hydrogens):
>>>
>>> 1) Load H2CCH2 and click Rectify - pointless, but it illustrates the
>>> terminal alkene issue.
>>>
>>> 2) Load H2CO and replace O with N - this is an example of the N-H issue
>>> on an imine.
>>>
>>> 3) Load CH4 and replace an H with a C. The result is ethane. Replace an
>>> ethane H with a Cl. Do this with another ethane H. Now click Rectify.
>>> Subsequent Cl replacement add with what appears to be a C-H bond length.
>>>
>>> 4) Load H2CCH2 and replace one of the carbons with O. Click Rectify. This
>>> is another example of problem 1 (above), but it illustrates a problem with
>>> what I would like to do. Specifically, make rectify an automatic part of any
>>> change.
>>>
>>> A note on point 4: Loading methane, building this to propane, and
>>> changing this to dimethy ether woks very nicely with rectify automatically
>>> hooked in. It has the visual feel of working with a model kit. In addition,
>>> building using a single bond framework seems to work just fine in general.
>>> You must, of course, be careful not to run new atoms into bonding distance
>>> of existing atoms.
>>>
>>> 5) Load methane. Replace a hydrogen with nitrogen. Do not click Rectify!
>>> Either click my UFF link on the page or type minimize in the text window
>>> (Run link to execute).
>>>
>>> If you repeat 5 above, but click Rectify before minimize, then the
>>> minimize will no longer separate the coincident H's on N. This appears to be
>>> a general problem: minimize will not work after a rectify. The problem here
>>> is that an automatic rectify after each substitution is, from my point of
>>> view, desirable.
>>>
>>> I hope my lack of specific instructions on the Web page is not a problem
>>> for you. Let me know if you need more information. If ftp access to our
>>> server would be of use to you, I'd be happy to send the information via a
>>> direct note.
>>>
>>> Finally, you are correct delete by atomIndex does work. I'm not sure why
>>> I had a problem with this.
>>>
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> http://chemagic.org
>>>
>>>
>>> ------------------------------------------------------------------------------
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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
>> [email protected]
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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
> [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
------------------------------------------------------------------------------
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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