diff --git a/ext/BioStructuresBioAlignmentsExt.jl b/ext/BioStructuresBioAlignmentsExt.jl
index 9ec97c4a..dd0c1c68 100644
--- a/ext/BioStructuresBioAlignmentsExt.jl
+++ b/ext/BioStructuresBioAlignmentsExt.jl
@@ -66,7 +66,9 @@ function BioStructures.Transformation(el1::StructuralElementOrList,
     for (i1, i2) in zip(inds1, inds2)
         sel_ats1 = collectatoms(res1[i1], alignatoms)
         sel_ats2 = collectatoms(res2[i2], alignatoms)
-        if length(atoms1) == length(atoms2)
+        # Ensure `atoms1` and `atoms2` have the same length, ignore residues
+        # where the number of atoms differ.
+        if length(sel_ats1) == length(sel_ats2)
             append!(atoms1, sel_ats1)
             append!(atoms2, sel_ats2)
         end