Don't reference out-of-range residues

Previously we were careless about whether
residue numbers were actually in range, but
now python-ihm checks for that.

modules/mmcif/pyext/src/data.py

@@ -388,7 +388,7 @@ class _StartingModel(ihm.startmodel.StartingModel):
     def __init__(self, asym_unit, struc_prov):
         self.filename = struc_prov[0].get_filename()
         super().__init__(
-            asym_unit=asym_unit(0, 0),  # will update in _add_residue()
+            asym_unit=asym_unit(1, 1),  # will update in _add_residue()
             # will fill in later with _set_sources_datasets()
             dataset=None,
             asym_id=struc_prov[0].get_chain_id(),

modules/mmcif/test/test_data.py

@@ -397,7 +397,7 @@ def test_coordinate_handler_get_structure_particles_nonseq(self):
     def test_coordinate_handler_add_chain(self):
         """Test CoordinateHandler.add_chain()"""
         s = ihm.System()
-        ent = ihm.Entity('ACGT')
+        ent = ihm.Entity('ACGTACGT')
         # Check that IMP residue numbering (11-18) maps to IHM (1-8)
         asym = ihm.AsymUnit(ent, auth_seq_id_map=10)
         m = IMP.Model()

modules/mmcif/test/test_restraints.py

@@ -247,8 +247,8 @@ def test_all_restraints_cross_link(self):
         """Test _AllRestraints with cross-link restraint"""
         conv = IMP.mmcif.Writer()
         m = IMP.Model()
-        h = make_model(m, chains=[("Rpb1", "AMT", "X"),
-                                  ("Rpb2", "ACC", "Z")])
+        h = make_model(m, chains=[("Rpb1", "A" * 50, "X"),
+                                  ("Rpb2", "C" * 50, "Z")])
         conv.add_model([h], [])
 
         xl_csv = self.get_input_file_name('test.xlms.csv')