Hi Mark--

> 
> thanks for the corrections to the script. I am seeing that the ZN
> atom does not have valid coordinates (below). I pasted my current
> script below. Also, is there something I need to do to fix the same
> errors for the termini, or should I not worry about them.
> 

Please try adding this snippet before writing out the coordinates:

try:
    protocol.addUnknownAtoms()
except protocol.CovalentViolation::
    pass


Charles

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