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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