On Thu, 18 Mar 2010, Angel Herr?ez wrote:
So you're saying that the color part is an entirely separate command?
Certainly. Once you define bonds, they are treated as such, and
that's the command.
However, I would advise you not to use bonds for this. You can draw
objects (lines, cylinders), and they will be treated separately by
Jmol.
For example, if you use connect, your connections will be altered by
any user that opens the popup menu and changes the style. If you use
draw, you retain control over them (and the chemical meaning is
preserved).
The command is "draw". I think you'd be OK with just lines. And you
can color them as you draw them (hopefully) or later.
Example:
draw diameter 0.2 {atomno=442} {atomno=410} color cyan;
Ah -- this sounds better! Since I want to draw things that are not
actually bonds, I guess they shouldn't be bonds in the Jmol world.
I just tried that worked for me -- I think that is the answer.
Thanks much!
Kent
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