Are these going in as t
Aidan Heerdegen wrote:
[I am resending this message as it hasn't appeared on the list yet,
apologies if you get two copies]
Re: Unable to make bonds between models (frames)
This is a feature. You cannot connect two atoms in different frames.
Each frame is a separate model, and bonds are part of models, so it
gets way too
messy to consider bonds between models.
As I thought. I use this feature, I just wasn't sure if it was possible
to *force* Jmol to make bonds between frames. It's not. I'm fine with that.
Solution #1:
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.
And yes, there are four frames. I can do this:
select (atomno=1 and model=1), (atomono=30 and model=2)
color yellow
and see the two atoms coloured appropriately. So no problems with my
selection syntax.
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
Solution #3:
Put them all in one file, turn autobonding off, load the file, use
connect, perhaps:
connect 1.0 1.5 (atomno<=30) (atomno<=30)
connect 1.0 1.5 (atomno>30) (atomno>30)
(that will take some experimentation)
and whatever additional connections you want between the sets.
Yes, I am sure that would work. I'm not sure I want to do it that way if
there is an alternative.
This sort of brings me back to the mol2 format question. I have all my
molecules in mol2 format, with all the bonding already sorted out. If I
(or someone else) wrote a mol2 format parser, is the default behavour in
Jmol to respect the bonding information contained in a file, or would
autobonding be turned on by default?
Thanks for your suggestions by the way, and for all the work by yourself
and the Jmol developers.
Cheerio
Aidan
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--
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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
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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