I don't know. I cannot reproduce your error:
in jmol-14.4.0_2015.10.14.zip I get:
$ load =1deh;
x={1:A}.xyz;
y={2:A}.xyz;
print (x+y)/2
OXIDOREDUCTASE 14-OCT-95 1DEH
CRYSTALLIZATION OF HUMAN BETA1 ALCOHOL DEHYDROGENASE (15
MG/ML) IN 50 MM SODIUM PHOSPHATE (PH 7.5), 2.0 MM NAD+ AND
1 MM 4-IODOPYRAZOLE AT 25 OC, 13% (W/V) PEG 8000
found biomolecule 1: A, B
{15.324988 11.581345 1.6729763}
Bob
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