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For empty alignments, rSuperimposeNucleotides uses the sequence alignment for the basis of creating the display. Model 1 and Model 3 should be empty in this case.
Don't display Jmol for empty alignments.
Verify that PDB files are correctly generated.
Example: http://rna.bgsu.edu/r3dalign/results/51f1576c5209c#.UfFXlayAG9K
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