Phenix bundle: module 'chimerax.phenix' has no attribute 'bundle_api'

[lukaszm002@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Hello
It looks i can not connect to phenix even though the bundle says installled in the tool shed.

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Phenix' custom initialization failed  
warning | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 511, in _get_api  
bundle_api = getattr(m, 'bundle_api')  
AttributeError: module 'chimerax.phenix' has no attribute 'bundle_api'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 364, in initialize  
api = self._get_api(session.logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 514, in _get_api  
raise ToolshedError("missing bundle_api for bundle \"%s\"" % self.name)  
chimerax.core.toolshed.ToolshedError: missing bundle_api for bundle "ChimeraX-
Phenix"  
  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Updates

> toolshed show

Downloading bundle ChimeraX_Phenix-0.3-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3.1  
[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip
install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing d:\pobrane\chimerax_phenix-0.3-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Core>=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Phenix==0.3) (1.5)  
Requirement already satisfied: ChimeraX-Atomic>=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Phenix==0.3) (1.41.5)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.2)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.0.2)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.0)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.0.1)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.0.3)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=8.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (8.0.3)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.6.8)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.8)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.2.2)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.9.1)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.5.1)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0)  
Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.24.3)  
Requirement already satisfied: ChimeraX-IO~=1.0.1 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PDB~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.1.2)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.10)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.1.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.1.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0.1)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.3)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (2.0)  
ChimeraX-Phenix is already installed with the same version as the provided
wheel. Use --force-reinstall to force an installation of the wheel.  
\---  

No bundles were installed  
Installed ChimeraX-Phenix (0.3)  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 511, in _get_api  
bundle_api = getattr(m, 'bundle_api')  
AttributeError: module 'chimerax.phenix' has no attribute 'bundle_api'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 364, in initialize  
api = self._get_api(session.logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 514, in _get_api  
raise ToolshedError("missing bundle_api for bundle \"%s\"" % self.name)  
chimerax.core.toolshed.ToolshedError: missing bundle_api for bundle "ChimeraX-
Phenix"  
  

ChimeraX-Phenix (installed) [version: 0.3] [api package: chimerax.phenix]
[category: General] [command: phenix connect [categories: General] [synopsis:
Connect to the Phenix command server.]] [command: phenix get restraints
[categories: General] [synopsis: Get Engh and Huber cif restraints for a
ligand.]] [command: phenix fit ligand [categories: General] [synopsis: Fit a
ligand into density.]] [command: phenix version [categories: General]
[synopsis: Report the current Phenix version.]]: custom initialization failed  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 511, in _get_api  
bundle_api = getattr(m, 'bundle_api')  
AttributeError: module 'chimerax.phenix' has no attribute 'bundle_api'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 318, in _register_cmd  
api = self._get_api(logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 514, in _get_api  
raise ToolshedError("missing bundle_api for bundle \"%s\"" % self.name)  
chimerax.core.toolshed.ToolshedError: missing bundle_api for bundle "ChimeraX-
Phenix"  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2216, in lazy_register  
deferred.call()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2147, in call  
return self.proxy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 309, in cb  
s._register_cmd(ci, logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 321, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
phenix version in bundle ChimeraX-Phenix:  
missing bundle_api for bundle "ChimeraX-Phenix"  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2832, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2568, in _find_command_name  
what.lazy_register(cmd_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2218, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'phenix version' failed
(register_command() failed for command phenix version in bundle ChimeraX-
Phenix:  
missing bundle_api for bundle "ChimeraX-Phenix")  
  
RuntimeError: delayed command registration for 'phenix version' failed
(register_command() failed for command phenix version in bundle ChimeraX-
Phenix:  
missing bundle_api for bundle "ChimeraX-Phenix")  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2218, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 511, in _get_api  
bundle_api = getattr(m, 'bundle_api')  
AttributeError: module 'chimerax.phenix' has no attribute 'bundle_api'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 318, in _register_cmd  
api = self._get_api(logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 514, in _get_api  
raise ToolshedError("missing bundle_api for bundle \"%s\"" % self.name)  
chimerax.core.toolshed.ToolshedError: missing bundle_api for bundle "ChimeraX-
Phenix"  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2216, in lazy_register  
deferred.call()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2147, in call  
return self.proxy()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 309, in cb  
s._register_cmd(ci, logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 321, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
phenix connect in bundle ChimeraX-Phenix:  
missing bundle_api for bundle "ChimeraX-Phenix"  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2832, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2568, in _find_command_name  
what.lazy_register(cmd_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2218, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'phenix connect' failed
(register_command() failed for command phenix connect in bundle ChimeraX-
Phenix:  
missing bundle_api for bundle "ChimeraX-Phenix")  
  
RuntimeError: delayed command registration for 'phenix connect' failed
(register_command() failed for command phenix connect in bundle ChimeraX-
Phenix:  
missing bundle_api for bundle "ChimeraX-Phenix")  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2218, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 451.67
OpenGL renderer: GeForce GTX 1650 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: pl_PL.cp1250
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Acer
Model: Nitro AN515-55
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 17,002,713,088
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10300H CPU @ 2.50GHz
OSLanguage: pl-PL

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-ISOLDE: 1.5
    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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

[Tristan Croll]

Eric, I vaguely recall a discussion from maybe 6 months back about removing this bundle from the ToolShed in favour of the new official ChimeraX-produced one. I was assuming this had happened - or is it something I need to do myself?

[Eric Pettersen]

I think that was because of a possible bundle-name collision. Decided to name my bundle PhenixUI and thus avoid that. I didn't think the bundles did the same things so didn't remove yours. However, if it's actually non-functional I certainly could remove it...

[Tristan Croll]

I haven't touched it since the R24 grant started working on the new one, so
I'm not surprised it's broken by now. On the whole I think it would be best
to remove it to avoid confusion.

On Thu, Jan 19, 2023 at 9:46 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Eric Pettersen]

Okay, I have nuked the Phenix bundle.