[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
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?
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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