Dear Charles,

I tried both approaches (1) wrefine_Zn.py & (2) wrefine_Zn_cs.py (below), but 
both give what might be the same error (with the errors at the bottom) and 
might be due to the way the indentation of the “try’ block is written in my 
scripts (4 spaces)?

end


""")

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



could you give me some pointers?

I attach the directory with the scrips and input files.

Thanks again for all your help with this.

Best,

Mark

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