From 987e812e23f4e361f4ca3de7d725530fe7736f7a Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Wed, 21 Oct 2026 14:23:38 +0200 Subject: [PATCH] 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 Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu --- tools/battery/still_battery.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tools/battery/still_battery.py b/tools/battery/still_battery.py index 67276774b..57bb93a0b 100644 --- a/tools/battery/still_battery.py +++ b/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: