id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1768 mmCIF export: chain ID KeyError lpravda@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-03-12) Description mmcif file export Log: UCSF ChimeraX version: 0.9 (2019-03-12) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/lpravda/assembly.cif Summary of feedback from opening /Users/lpravda/assembly.cif --- warnings | Atom H1 is not in the residue template for GLN #1 in chain A Mismatched number of atoms (530 vs. 531) Mismatched number of atoms (530 vs. 531) Mismatched number of atoms (530 vs. 531) Mismatched number of atoms (530 vs. 531) Mismatched number of atoms (530 vs. 531) 4 messages similar to the above omitted Chain information for assembly.cif --- Chain | Description 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | copper (I) ion Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 813, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 576, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 141, in display fmt.save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 40, in save return self._save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 66, in fmt.export(ses, _add_missing_suffix(fn, fmt), fmt.name)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 203, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 61, in save_file return mmcif_write.write_mmcif(session, path, models=models) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 108, in write_mmcif save_structure(session, f, models, used_data_names) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 516, in save_structure asym_id, entity_id = het_asym_info[r.mmcif_chain_id] KeyError: 'B' KeyError: 'B' File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 516, in save_structure asym_id, entity_id = het_asym_info[r.mmcif_chain_id] See log for complete Python traceback. OpenGL version: 4.1 ATI-2.4.10 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc. File attachment: assembly.cif.gz }}} [attachment:""assembly.cif.gz""] " defect closed normal Input/Output fixed all ChimeraX