Bob Hanson wrote:
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?
I'm with Miguel, rendering may be an issue of the hbonds command. hbonds
on should be default which may be
hbonds 1
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.
should be altered to
hbonds 1
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.
That is an argument, but in this case we should render with default
values of do not render any kind of newly generated bonds. I vote for
using default values.
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.
simply use
wireframe 0.15
and change default values
hbonds 1
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.
side effect of connect should be to
set bondmode AND
and select the newly (dis)connected atoms
or which may be better, define a set
define CONNECT <AND-atoms>
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
I think, in most cases, there are multiple connect expressions needed to
render an experimental structure (the bond length are not as optimal to
do this with two simple distance criteria statements) and bond rendering
is done afterwards.
If special rendering for double bonds is desired, the CONNECT sets could
be stored till a final rendering commands altered the default visualization.
...
define double1 CONNECT
...
select double1
wireframe 0.1
select double2
wireframe 0.1
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
^ this may *not* be the same as the following
to
connect 1.3 2.0 HBOND NEW 2 (hydrogen) (oxygen)
I'd rather have the latter.
I vote for:
define CONNECT <AND-atoms>
and a distinct radius of hbonds 1 (dotted line) by default.
Regards, Jan
...
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