Raised meaningful error for short peptide stretch

package/CHANGELOG

@@ -20,6 +20,9 @@ The rules for this file:
  * 2.11.0
 
 Fixes
+ * DSSP now explicitly checks for a minimum of 6 residues and raises a clear
+   error message, unlike the previous behavior where it would fail with an
+   incomprehensible broadcasting error at execution time (Issue #5046, PR #5163)
  * Fixes the verbose=False in EinsteinMSD, and only shows progress bar when
    verbose=True (Issue #5144, PR #5153)
  * Fix incorrect assignment of topology_format to format (and vice versa)

package/MDAnalysis/analysis/dssp/dssp.py

@@ -210,7 +210,7 @@ class DSSP(AnalysisBase):
     Parameters
     ----------
     atoms : Union[Universe, AtomGroup]
-        input Universe or AtomGroup. In both cases, only protein residues will
+        input Universe or AtomGroup with at least 6 protein residues. In both cases, only protein residues will
         be chosen prior to the analysis via `select_atoms('protein')`.
         Heavy atoms of the protein are then selected by name
         `heavyatom_names`, and hydrogens are selected by name
@@ -239,6 +239,8 @@ class DSSP(AnalysisBase):
 
     Raises
     ------
+    ValueError
+        If fewer than 6 residues are provided in the selection.
     ValueError
         if ``guess_hydrogens`` is True but some non-PRO hydrogens are missing.
 
@@ -357,6 +359,12 @@ def __init__(
                 )
             )
 
+        if len(ag.residues) < 6:
+            raise ValueError(
+                "DSSP requires at least 6 residues for secondary structure analysis, "
+                f"but only {len(ag.residues)} residue(s) were provided in the selection."
+            )
+
     def _prepare(self):
         self.results.dssp_ndarray = []
 

testsuite/MDAnalysisTests/analysis/test_dssp.py

@@ -89,3 +89,24 @@ def test_exception_raises_with_atom_index(pdb_filename, client_DSSP):
         match="Residue <Residue SER, 298> contains*",
     ):
         DSSP(u, guess_hydrogens=False).run(**client_DSSP)
+
+
+def test_insufficient_residues_raises_error(client_DSSP):
+    """Test that DSSP raises clear error for insufficient residues."""
+    u = mda.Universe(TPR, XTC)
+
+    protein = u.select_atoms("protein")
+    resids = protein.residues.resids
+
+    with pytest.raises(ValueError, match="DSSP requires at least 6 residues"):
+        res2 = protein.residues[:2].atoms
+        DSSP(res2)
+
+    with pytest.raises(ValueError, match="DSSP requires at least 6 residues"):
+        res4 = protein.residues[:4].atoms
+        DSSP(res4)
+
+    res6 = protein.residues[:6].atoms
+    dssp = DSSP(res6)
+    result = dssp.run(**client_DSSP, stop=1)
+    assert result.results.dssp.shape[1] == 6