Hens Borkent wrote:
To follow up on this:
I realized that the suggestion to interpret partail01 as an hbond wasn't
such a good idea, as hbonds are drawn as thin lines.
However, when I checked Bob's 10.1 demo page I noticed something odd (to
me).
The last caffeine command CONNECT MODIFY HBOND turns all the existing
single bonds (between atoms selected in the previous command) into thick
partial single bonds. So these still "exist".
The comment says "#modified hbonds take previous bond's diameter", but
it seems the other way around, "#previous bonds take hbond appearance".
Do I interpret this correctly?
Sure, either interpretation is correct. Technically, as far as Jmol is
concerned, they are now hydrogen bonds. Thick hydrogen bonds. :)
And, can the CML bondtype partial01 be drawn again as a partial single
bond with default wireframe value?
I'll let others answer that. The more long-term solution would be to
drop the hydrogen bond idea -- they aren't hydrogen bonds -- and to
implement a "partial bond" idea. That's fairly complex. Please enter
it as a feature request if you like the idea.
Bob
Hens
Sorry for bringing this up rather late, but I noticed that with all
the recent changes in the bond features one of my favourites got lost:
in reaction mechanisms I use the "partial01" bond type as defined in a
cml structure file. It was drawn as a dashed bond, now it is displayed
as a single bond.
Maybe it is solved if the partial01 bond in a CML file is interpreted
as a hbond?
Hens
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
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