[MMTK] Copy/Replace Operations

[tezcan at ecs.umass.edu]

Hi,
I am trying to modify/transform a sidechain of a residue, save it and  
replace sidechains with modified versions as necessary.
Following might give you a better idea of what I am trying to  
do:(suppose I have a function called modify()):

original=deepcopy(universe.protein[0][1].sidechain)
universe.protein[0][1].modify()
modified=deepcopy(universe.protein[0][1].sidechain)
#now suppose I need the original back or want to replace it with  
another version
universe.protein[0][1].sidechain=original

I have tried few different ways to do this but I get crazy results  
from universe.energy(universe.protein[0][1]) after replacement, so I  
know I am doing something wrong. What is the proper way of doing this  
type of copy/replace operations in MMTK?
Thanks for your help.
Gokhan