id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3097 Undeposited structure: 'NoneType' object has no attribute 'isupper' Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 0.93 (2020-04-03) Description Offending PDB file is at https://github.com/thorn-lab/coronavirus_structural_task_force/blob/master/pdb/3c_like_proteinase/SARS-CoV-2/5reb/validation/pdb-redo/5reb_final.pdb Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5reb.cif Summary of feedback from opening 5reb.cif --- note | Fetching CCD T0Y from http://ligand-expo.rcsb.org/reports/T/T0Y/T0Y.cif 5reb.cif title: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434899 [more info...] Chain information for 5reb.cif #1 --- Chain | Description A | SARS-CoV-2 main protease Non-standard residues in 5reb.cif #1 --- DMS — dimethyl sulfoxide T0Y — 1-[(thiophen-3-yl)methyl]piperidin-4-ol 5reb.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly > open 5reb.pdb 5reb.pdb title: Pandda analysis group deposition -- crystal structure of sars-cov-2 main protease In complex with Z2856434899 [more info...] Chain information for 5reb.pdb #2 --- Chain | Description A | sars-cov-2 main protease Non-standard residues in 5reb.pdb #2 --- DMS — dimethyl sulfoxide T0Y — 1-[(thiophen-3-yl)methyl]piperidin-4-ol > hide #1 models > show #1 models > open2 /home/tic20/my- > gits/coronavirus_structural_task_force/pdb/3c_like_proteinase/SARS- > CoV-2/5reb/old/5reb.pdb 5reb.pdb title: Pandda analysis group deposition -- crystal structure of sars-cov-2 main protease In complex with Z2856434899 [more info...] Chain information for 5reb.pdb #3 --- Chain | Description A | main protease Non-standard residues in 5reb.pdb #3 --- DMS — dimethyl sulfoxide T0Y — 1-[(thiophen-3-yl)methyl]piperidin-4-ol > hide #1 models > hide #2 models > open2 /home/tic20/my- > gits/coronavirus_structural_task_force/pdb/3c_like_proteinase/SARS- > CoV-2/5reb/old/5reb.cif 5reb.cif title: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434899 [more info...] Chain information for 5reb.cif #4 --- Chain | Description A | main protease Non-standard residues in 5reb.cif #4 --- DMS — dimethyl sulfoxide T0Y — 1-[(thiophen-3-yl)methyl]piperidin-4-ol 5reb.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly > open2 /home/tic20/my- > gits/coronavirus_structural_task_force/pdb/3c_like_proteinase/SARS- > CoV-2/5reb/validation/pdb-redo/5reb_final.pdb Chain information for 5reb_final.pdb #5 --- Chain | Description A | main protease In complex with Z2856434899 Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/dialog.py"", line 146, in _qt_safe if data_format is None else "" format "" + StringArg.unparse(data_format.nicknames[0]))) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 86, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 166, in provider_open session.models.add(opened_models) File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/models.py"", line 588, in add m.added_to_session(session) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1143, in added_to_session self._report_res_info(session) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1410, in _report_res_info res_info = self.get_formatted_res_info(standalone=True) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 250, in _get_formatted_res_info return format_nonstd_res_info(model, update_nonstd, standalone) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 287, in format_nonstd_res_info formatted = fmt_component(abbr, name, synonyms) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 272, in fmt_component text += process_chem_name(syns) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 330, in process_chem_name if name.isupper() and ("" "" in name or len(name) > 5): AttributeError: 'NoneType' object has no attribute 'isupper' AttributeError: 'NoneType' object has no attribute 'isupper' File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 330, in process_chem_name if name.isupper() and ("" "" in name or len(name) > 5): See log for complete Python traceback. > pwd Current working directory is: /home/tic20/my- gits/coronavirus_structural_task_force/pdb/3c_like_proteinase/SARS-CoV-2/5reb OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia }}} " defect closed normal Input/Output fixed all ChimeraX