[MMTK] Collection.findTransformation()

Konrad Hinsen hinsen@cnrs-orleans.fr
Tue, 27 May 2003 22:29:22 +0200


On Tuesday 27 May 2003 20:45, you wrote:
> The way I'm doing it doesn't generate any error messages.  The

I just checked: I have fixed that in my working code a while ago. In the =
next=20
release, you will get an error message.

> file.  Since these aren't the same Residues, or even the same
> PeptideChain, would your suggested method still work?  If so, how do I =
do

Yes. In principle it works as follows (untested code!):

universe =3D InfiniteUniverse()
universe.protein =3D Protein('foo.pdb')
residue1 =3D universe.protein[0][0]
residue2 =3D universe.protein[0][1]  # or whatever you want

conf1 =3D universe.configuration()
conf2 =3D Configuration(universe)
for name1, name2 in [('C', 'C'), ('C_alpha', 'N')]:
    atom1 =3D getattr(residue1.peptide, name1)
    atom2 =3D getattr(residue2.peptide, name2)
    conf2[atom1] =3D atom2.position()

tr, rms =3D residue1.findConfiguration(conf2)

No reference is ever made to the universe of residue2, so this works in a=
ny=20
situation.

Konrad.
--=20
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