Bob Hanson wrote:
Aidan Heerdegen wrote:
You can set up measurements between frames, and if you turn off the
numbers, then it looks a lot like what you are asking for.
Sounds fine. I might even want the numbers, but I can't get it to
work with 10.2.0, the trunk version via subversion or your
branches/bob200603 version. I can make a measurement between atoms in
the same frame, but different frames, no dice.
I use syntax like this:
measure 1.0 20.0 (atomno=1 and model=1) (atomono=30 and model=1)
#worked in bob200603
measure 1.0 20.0 (atomno=1 and model=1) (atomono=30 and model=2)
#didn't work in bob200603
OK, I consider that a bug, since you can do it by clicking on atoms.
It is fixed now. In the latest version at
http://www.stolaf.edu/people/hansonr/jmol/test/proto that works. Just
be sure in each set you are selecting ONE specific atom -- as you are.
If you were to do
measure all (atomno=1) (atomno=2)
then it will only draw lines between atom 1 and atom 2 in each model
independently. But if you do
measure (atomno=1 and */1) (atomno=2 and */2)
then you will get a line, because each of these specifies a SINGLE
atom -- thus not ambiguous and clearly what someone wants.
Thanks. This works just as I would want it to ... but ... I can't
colour measurements differently. I would like to colour code my
non-bonded contacts to make it easier to differentiate between them.
Solution #2:
In addition, you can (in 10.x) draw lines that look a lot like bonds
between any
two atoms, regardless of their frame. But I don't think that's the
best solution.
I don't know, that sounds pretty good to me. I'd like to colour them
for identification, turn them on and off etc. What is this new
feature called? Is this in the bob200603 branch?
I'm wrong. You can't do that right now with draw objects -- they are
model specific.
draw [idname] [magnitude_percent] [starting point] [ending point]
e.g.
draw myline 100 (atomno=1) (atomno=30)
color $myline translucent red
Darn. That looked like the one for me. I particularly like the
variable-like naming. Makes it very easy to turn them on and off.
I think I will ditch the separate frames idea, use drawing and hope to
make use of selecting by molecule.
Another more general question: Is all the functionality that you
currently demonstrate with the Applet on your web pages going to be
accessible in the Jmol application via the scripting interface? I am
thinking about what approach I will take, and if the Applet is likely
to have a richer interface then I will probably use that.
Thanks for your help,
Cheerio
Aidan
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