Re: [Jmol-users] delete hydrogens minimize addHydrogens

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

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 <ot...@ch...>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