still battery: dimple gets PDB-format coordinates converted from an mmCIF-only deposition

dimple refuses an mmCIF model ("neither mtz nor pdb"), so a set whose deposition exists only as mmCIF
lost its REFMAC R-free; the coordinates are converted with gemmi first.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu

tools/battery/still_battery.py

@@ -217,6 +217,9 @@ def refine(wd, e, cache):
     if free is None:
         return None, None, "no free set in the deposition"
     env = model_check.ccp4_env()
+    if xyz.endswith(".cif"):  # dimple takes PDB-format coordinates only
+        subprocess.run(["gemmi", "convert", xyz, "deposited.pdb"], cwd=wd, env=env, capture_output=True)
+        xyz = os.path.join(wd, "deposited.pdb")
     subprocess.run(["reindex", "hklin", "p.mtz", "hklout", "p_sg.mtz"], cwd=wd, env=env,
                    input=f"SYMM '{e['sg']}'\nEND\n", capture_output=True, text=True)
     with open(os.path.join(wd, "dimple.out"), "w") as log: