id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1916 KeyError saving mmCIF c.sachse@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-18.5.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-05-05) Description Problem saving of helical assembly TMV in mmcif format. assembly was expanded according to BIOMT matrix from PDB code 4udv (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.9 (2019-05-05) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/sachse/sciebo/Shared/temp_shared/kkaspary/tmv_49x.pdb tmv_49x.pdb title: Cryo-em structure of TMV At 3.35 A resolution [more info...] Chain information for tmv_49x.pdb --- Chain | Description 1.1/A | capsid protein 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 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A 1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A 1.35/A 1.36/A 1.37/A 1.38/A 1.39/A 1.40/A 1.41/A 1.42/A 1.43/A 1.44/A 1.45/A 1.46/A 1.47/A 1.48/A 1.49/A | capsid protein 1.1/R 1.2/R 1.3/R 1.4/R 1.5/R 1.6/R 1.7/R 1.8/R 1.9/R 1.10/R 1.11/R 1.12/R 1.13/R 1.14/R 1.15/R 1.16/R 1.17/R 1.18/R 1.19/R 1.20/R 1.21/R 1.22/R 1.23/R 1.24/R 1.25/R 1.26/R 1.27/R 1.28/R 1.29/R 1.30/R 1.31/R 1.32/R 1.33/R 1.34/R 1.35/R 1.36/R 1.37/R 1.38/R 1.39/R 1.40/R 1.41/R 1.42/R 1.43/R 1.44/R 1.45/R 1.46/R 1.47/R 1.48/R 1.49/R | 5'-D(*GP*ap*ap)-3' > save /Users/sachse/sciebo/Shared/temp_shared/kkaspary/tmv_49x.mmcif Traceback (most recent call last): File ""/Applications/Science/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/tool.py"", line 140, in lambda e, what=what, self=self: self.handle_scheme(what), File ""/Applications/Science/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/tool.py"", line 96, in handle_scheme run(self.session, f'{value}') File ""/Applications/Science/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/Science/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2631, in run result = ci.function(session, **kw_args) File ""/Applications/Science/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/Applications/Science/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""/Applications/Science/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/Science/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/Science/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 508, in save_structure asym_id, entity_id = asym_info[(chain_id, chars)] KeyError: ('A', 'SYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTSGPAT') KeyError: ('A', 'SYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTSGPAT') File ""/Applications/Science/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 508, in save_structure asym_id, entity_id = asym_info[(chain_id, chars)] See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.8.38 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. }}} " defect closed normal Input/Output fixed Eric Pettersen all ChimeraX