Bob-
OK, I think I see something consistent in the delete problem now:
Delete followed by "minimize addHydrogens" works if the deleted hydrogen is
the only hydrogen on the multivalent atom. In every other case I look at, I
see it failing:
I'll use methanol to exemplify this, but I think it's pretty general:
1) Delete the alcohol H, and you can put it back on.
2) Delete 1 methyl H, and you cannot put it back on.
3) Delete 2nd methyl H, and you cannot put it (or the first deleted) back
on.
4) Delete final methyl H, and you can put them all back on.
Otis
On Fri, Feb 26, 2010 at 2:50 PM, Otis Rothenberger <o...@chemagic.com>wrote:
> Bob-
>
> Using your approach, picking deletes an H on propane. But minimize
> addHydrogens does not add it back. I'm thinking maybe I have the wrong Jmol
> version. I'm using 11.9.30_dev 2010-02-12 12:26. Is this the wong version?
>
> The two minimization steps simply reflect the fact that I forgot "calculate
> hydrogens" was an option. I also need to clean the multi-step calls to
> jmoScript(). That goes back to when I thought I had timing problems. I was
> playing with delays in various parts of the script, and breaking things
> apart was just a convenience.
>
> evalRasol is history! How about sortOutOtisConvolutedWayOfDoingThings() for
> the replacement. :) I guess I'll just use processJmol(). Actually, the
> function processes Jmol and JavaScipt entered in the page's text field.
>
>
> Otis
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>
--
Otis Rothenberger
http://chemagic.org
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