ArtiaX: problem loading Star file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> artiaX

Unknown command: artiaX  

> ui tool show "Selection Inspector"

> toolshed reload available

> toolshed install ArtiaX

ChimeraX-ArtiaX (0.3) is already installed  

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened YTC009_3_lam7_ts2_corrected.mrc as #1.1.1, grid size 682,960,234, pixel
15.8,15.8,15.8, shown at level 0.241, step 1, values float32  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> undo

> hide #!1.1.1 models

> show #!1.1.1 models

> artiax view xy

> open
> /Users/ramtinhosseini/Downloads/yeast_ribosomes/coordinates/YTC009_3_lam7_ts2_corrected_80S_ref.star
> format star

Traceback (most recent call last):  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/formats.py", line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/io.py", line 35, in open_particle_list  
data = formats[format_name].particle_data(session, file_name, oripix=1,
trapix=1, additional_files=additional_files)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 120, in
__init__  
super().__init__(session, file_name, oripix=oripix, trapix=trapix,
additional_files=additional_files)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/ParticleData.py", line 441, in __init__  
self.read_file()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 123, in
read_file  
content = starfile.read(self.file_name, always_dict=True)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/functions.py", line 24, in read  
star = StarParser(filename, read_n_blocks=read_n_blocks)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 30, in __init__  
self.parse_file()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 38, in parse_file  
self._parse_data_block()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 54, in _parse_data_block  
self._parse_loop_block()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 77, in _parse_loop_block  
df = self._parse_loop_data()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 177, in _parse_loop_data  
df = pd.read_csv(  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/readers.py", line 912, in read_csv  
return _read(filepath_or_buffer, kwds)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/readers.py", line 583, in _read  
return parser.read(nrows)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/readers.py", line 1704, in read  
) = self._engine.read( # type: ignore[attr-defined]  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read  
chunks = self._reader.read_low_memory(nrows)  
File "pandas/_libs/parsers.pyx", line 814, in
pandas._libs.parsers.TextReader.read_low_memory  
File "pandas/_libs/parsers.pyx", line 875, in
pandas._libs.parsers.TextReader._read_rows  
File "pandas/_libs/parsers.pyx", line 850, in
pandas._libs.parsers.TextReader._tokenize_rows  
File "pandas/_libs/parsers.pyx", line 861, in
pandas._libs.parsers.TextReader._check_tokenize_status  
File "pandas/_libs/parsers.pyx", line 2029, in
pandas._libs.parsers.raise_parser_error  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
File "pandas/_libs/parsers.pyx", line 2029, in
pandas._libs.parsers.raise_parser_error  
  
See log for complete Python traceback.  
  

> artiax tomo #1.1.1 pixelSize 15.828000423845308

> artiax view xy

> artiax tomo #1.1.1 slice 127

> artiax tomo #1.1.1 slice 128

> open
> /Users/ramtinhosseini/Downloads/yeast_ribosomes/coordinates/YTC009_3_lam7_ts2_corrected_80S_ref.star
> format star

Traceback (most recent call last):  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/formats.py", line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/io.py", line 35, in open_particle_list  
data = formats[format_name].particle_data(session, file_name, oripix=1,
trapix=1, additional_files=additional_files)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 120, in
__init__  
super().__init__(session, file_name, oripix=oripix, trapix=trapix,
additional_files=additional_files)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/ParticleData.py", line 441, in __init__  
self.read_file()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 123, in
read_file  
content = starfile.read(self.file_name, always_dict=True)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/functions.py", line 24, in read  
star = StarParser(filename, read_n_blocks=read_n_blocks)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 30, in __init__  
self.parse_file()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 38, in parse_file  
self._parse_data_block()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 54, in _parse_data_block  
self._parse_loop_block()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 77, in _parse_loop_block  
df = self._parse_loop_data()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 177, in _parse_loop_data  
df = pd.read_csv(  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/readers.py", line 912, in read_csv  
return _read(filepath_or_buffer, kwds)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/readers.py", line 583, in _read  
return parser.read(nrows)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/readers.py", line 1704, in read  
) = self._engine.read( # type: ignore[attr-defined]  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read  
chunks = self._reader.read_low_memory(nrows)  
File "pandas/_libs/parsers.pyx", line 814, in
pandas._libs.parsers.TextReader.read_low_memory  
File "pandas/_libs/parsers.pyx", line 875, in
pandas._libs.parsers.TextReader._read_rows  
File "pandas/_libs/parsers.pyx", line 850, in
pandas._libs.parsers.TextReader._tokenize_rows  
File "pandas/_libs/parsers.pyx", line 861, in
pandas._libs.parsers.TextReader._check_tokenize_status  
File "pandas/_libs/parsers.pyx", line 2029, in
pandas._libs.parsers.raise_parser_error  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
File "pandas/_libs/parsers.pyx", line 2029, in
pandas._libs.parsers.raise_parser_error  
  
See log for complete Python traceback.  
  

> open
> /Users/ramtinhosseini/Downloads/yeast_ribosomes/coordinates/YTC009_3_lam7_ts2_corrected_80S_ref.star

Failed opening file
/Users/ramtinhosseini/Downloads/yeast_ribosomes/coordinates/YTC009_3_lam7_ts2_corrected_80S_ref.star:  
Error tokenizing data. C error: Expected 1 fields in line 12, saw 10  
  

> open
> /Users/ramtinhosseini/Downloads/yeast_ribosomes/coordinates/YTC009_3_lam7_ts2_corrected_80S_ref.star

Failed opening file
/Users/ramtinhosseini/Downloads/yeast_ribosomes/coordinates/YTC009_3_lam7_ts2_corrected_80S_ref.star:  
Error tokenizing data. C error: Expected 1 fields in line 12, saw 10  
  

> open
> /Users/ramtinhosseini/Downloads/yeast_ribosomes/coordinates/YTC009_3_lam7_ts2_corrected_80S_ref.star
> format star

Traceback (most recent call last):  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/formats.py", line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/io.py", line 35, in open_particle_list  
data = formats[format_name].particle_data(session, file_name, oripix=1,
trapix=1, additional_files=additional_files)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 120, in
__init__  
super().__init__(session, file_name, oripix=oripix, trapix=trapix,
additional_files=additional_files)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/ParticleData.py", line 441, in __init__  
self.read_file()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 123, in
read_file  
content = starfile.read(self.file_name, always_dict=True)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/functions.py", line 24, in read  
star = StarParser(filename, read_n_blocks=read_n_blocks)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 30, in __init__  
self.parse_file()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 38, in parse_file  
self._parse_data_block()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 54, in _parse_data_block  
self._parse_loop_block()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 77, in _parse_loop_block  
df = self._parse_loop_data()  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/starfile/parser.py", line 177, in _parse_loop_data  
df = pd.read_csv(  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/readers.py", line 912, in read_csv  
return _read(filepath_or_buffer, kwds)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/readers.py", line 583, in _read  
return parser.read(nrows)  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/readers.py", line 1704, in read  
) = self._engine.read( # type: ignore[attr-defined]  
File "/Users/ramtinhosseini/Library/Application Support/ChimeraX/1.6/site-
packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read  
chunks = self._reader.read_low_memory(nrows)  
File "pandas/_libs/parsers.pyx", line 814, in
pandas._libs.parsers.TextReader.read_low_memory  
File "pandas/_libs/parsers.pyx", line 875, in
pandas._libs.parsers.TextReader._read_rows  
File "pandas/_libs/parsers.pyx", line 850, in
pandas._libs.parsers.TextReader._tokenize_rows  
File "pandas/_libs/parsers.pyx", line 861, in
pandas._libs.parsers.TextReader._check_tokenize_status  
File "pandas/_libs/parsers.pyx", line 2029, in
pandas._libs.parsers.raise_parser_error  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
File "pandas/_libs/parsers.pyx", line 2029, in
pandas._libs.parsers.raise_parser_error  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.10.12
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
      OS Loader Version: 577~129

Software:

    System Software Overview:

      System Version: macOS 13.3 (22E252)
      Kernel Version: Darwin 22.4.0
      Time since boot: 1 day, 4 hours, 5 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    pandas: 2.0.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    starfile: 0.4.12
    superqt: 0.5.3
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0