it occurs to me, are we going to need to update bonds when this  
happens? i know very little about chemistry so i'm not too sure how  
this all works.

so i've mucked around with everything a bit, and it seems to refresh  
coordinates rather well. one issue i've noticed is that i often have  
to move the model after i call the javascript method to actually  
display the changes. in fact, with the build i've made of your branch  
(what seems to be the latest), this same problem occurs in your  
setAtomCoord method. any ideas?

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