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I have created program that generates positions of 150000 C atoms
(carbon structure), and using Jmol-11.6.18 I can see this structure. I
have generated only positions of atoms, and since bounds are
automatically generated by Jmol, I would like to export these bounds
information together with angles between bounds from Jmol to some
file. My question is how can I do it?
In order to get angles between bounds I have used
measure allconnected (*)(*)(*);
command, but is seems that it doesn't work for large structures (more
than 5000 of atoms). I didn't received any error message, but results
as well. In my case this command just utilized my CPU 100%. I have try
this on different platforms (Mac OS X, Linux) and result was the same.
Since I'm beginner in this field, I really don't know is Jmol
developed for this purposes? If it's not please could you recommend me
any good application which could do that?
Thanks and best regards, Dusan
Phone: +381 11 3713152
Fax: +381 11 3162190
Scientific Computing Laboratory
Institute of Physics Belgrade
Pregrevica 118, 11080 Belgrade, Serbia
Hello Dusan, and welcome to Jmol!
To export the model from Jmol to file, you can try this:
Open the script console (from pop-up menu > Console, or from the top menu > Script)
and type this:
more details here:
The MOL format includes bond information.
Regarding your question of measures, I cannot help, but somebody else will do.