Jan, mostly I'm with you. Howver, when a new bond is made, one must
have all the rendering associated with it. If one creates HBONDS, one
must at the same time associate a
rendering value to it -- the bond radius. Agreed?
Same goes for single, double, triple, aromatic.
I was wrong in how connect is behaving. Actually, the default value
for the radius rendering is "OFF" for HBOND and "0.15" for all others.
This is regardless of any previous select or wireframe or hbond command.
I'm all for separation of function, but CONNECT is a new issue,
because Jmol has prior to this never allowed new bonds to be formed
AFTER rendering.
The questions, then, include:
1) how do you those newly created bonds rendered?
2) do you want to be able to override the default values?
My personal answer is (1) I don't care, and (2) yes.
A purist would arue then that we should do a pure connect and not
render anything -- default hbond 0 and wireframe 0. But to me that
seems very odd -- connecting the bonds but not displaying them. It
just seems simpler to me to designate at the time of connecting
whether or not to accept the default rendering.
Another thought comes to mind. It's not clear how one would ever go
back and target those new bonds specifically for setting their radius
any other way. Remember, the only other way is by selecting atoms and
using "set bondmode" AND or OR to accomplish what one would want.
The interesting thing about connect is that it allows one to redefine
bonds in a new way. One might like, for example, to highlight bonds
between certain atoms this way. Just a thought.
I'm not a purist; I like simplicity. So if adding a single parameter
changes
connect 1.3 2.0 HBOND NEW (hydrogen) (oxygen)
select hydrogen and within(2.0, oxygen) and not within(1.3, oxygen)
or oxygen and within(2.0, hydrogen) and not within(1.3, hydrogen)
hbond 2
to
connect 1.3 2.0 HBOND NEW 2 (hydrogen) (oxygen)
I'd rather have the latter.
Jan wrote:
just like Rolf, I don't like radius within connect (and reading
documentation before using the command would prevent others from
repeating my mistake).
Regards, Jan
I don't think you made a mistake -- you used the command in a totally
natural way, expecting to see the same sort of results with HBOND as
you did with SINGLE. But it didn't behave the way you expected it to,
because the default for HBONDS is OFF. I take that to mean you were
right and the command was not optimal.
Bob
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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