missing pdb is not error not warning

xchem · Jan 30, 2024 · 25ba13d · 25ba13d
1 parent 1ed0fb9
commit 25ba13d
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/src/xchemalign/collator.py b/src/xchemalign/collator.py
@@ -377,9 +377,11 @@ def _validate_soakdb_input(self, input, crystals):
                         else:
                             expanded_files.append(None)
                             missing_files += 1
-                            self._log_warning(
-                                "PDB file for {} not found: {}. Skipping entry".format(xtal_name, full_inputpath)
+                            m = (
+                                "PDB file for {} not found: {}. "
+                                + "Add this to the inputs.exclude section of your config.yaml file if you want to continue"
                             )
+                            self._log_error(m.format(xtal_name, full_inputpath))
                             continue
 
                         # if we have a PDB file then continue to look for the others