[BioPython] Problem with Superimposer

Sergio E. Wong swon9 at itsa.ucsf.edu
Tue Jul 13 19:37:50 EDT 2004


Hi;

   I am trying to superimpose two crystal structures using the
Bio.PDB.Superimposer, following the example in the biopython FAQ
document where it explains how to do this.  For the purposes of testing, I
am only using 5 atoms in the atoms lists.  Below I show the two atom lists
and the error I get when I try to use the set_atoms method.

>>> ebg_res1
[<Atom N>, <Atom CA>, <Atom C>, <Atom O>, <Atom CB>]
>>> ebh_res1
[<Atom N>, <Atom CA>, <Atom C>, <Atom O>, <Atom CB>]
>>> sup.set_atoms( ebg_res1, ebh_res1)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
TypeError: unbound method set_atoms() must be called with Superimposer
instance as first argument (got list instance instead)


Does anyone have any idea of why this is happening?

Thanks

-Sergio


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