Jairav, I've had a couple ideas:
1. You can generate the necessary xyz coordinates by script
2. Using Jmol "connect" and then "minimize" commands can produce the wanted
approach of certain residues
Have a look at this:
http://www31.websamba.com/jpeg62/Jmol/gene_simulation.htm
I have used alpha carbons since I think that P-P bonds are quite longer and the
effect
is not so good. I also had to create bonds between the carbons so that the
minimize
algorithm doesn't pull them apart.
The PDB data is created with Javascript and loaded into Jmol inline. You just
tell it
how many nodes you want.
Then, the "go" button tells where to put connections and runs the minimization.
What do you think?
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