[MMTK] Collection.findTransformation()

[Kyle Krull]

	I am using MMTK's findTransformation to match some backbone atoms
from one residue onto another for residue substitution.  Specifically, I
am trying to match [C, C_alpha, C_beta] from one residue onto the same
group of atoms on another.
	Most of the time this works just fine, but in one case, the C from
one residue is matched to the C_beta of the other, and vice versa.  The
final mapping ends up being like this:

Residue1	Residue2
C		C_beta
C_alpha		C_alpha
C_beta		C

	Does anybody know what could cause this sort of error?  I've tried
looking at the code for findTransformationAsQuaternion(), but it's a bit
confusing to me.  What I need is for the atoms to be matched by name, but
I'm not sure if this is being done or not.

Thanks,
	Kyle Krull