Undeposited structure: 'NoneType' object has no attribute 'isupper'

[Tristan Croll]

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

[Eric Pettersen]

Fixed in the next build. The issue was with the HETNAM record for T0Y, where the actual compound name is blank. FYI, the FORMUL record for T0Y is also blank.

[Tristan Croll]

Not my doing - but the file comes from PDB-REDO which lots of people like to use. Not as good as it claims to be, to be honest - in this case it completely messed up the ligand by turning its piperidine ring aromatic. Another example of why it’s dangerous to trust automatic pipelines...