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covalent bond between symmetry related halves of a spermine molecule

Wed Feb 21 18:05:51 EST 1996

> I have an asymetric unit that contains half a spermine molecule.
> The other half is produced by the symmetry operators.
> The problem is, when I perform positional refinement on the asymetric
> unit the two halves of the molecule refine away from each other (start 
> at 1.54 angstrom apart and end up at 2.8 angstrom apart).
> How do I set things up so that X-PLOR recognises that these 2 symmetry
> related halves are covalently bound?

Here is an easy solution:
Build the entire ligand into density. The ligand 
will overlap onto itself due to the xtallographic axis. Set the occupacy
of the ligand to 0.5

Now, in your xplor script include this:

   INTERACTION (segid A) (segid A)
   INTERACTION (segid A) (segid L)

(assuming that the protein chain is called A and your ligand L)

In this regime, the enery between your ligand and itself won't
be calculated, so there will be no self repulsion.

Hope this helps,


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