ISOLDE installed into incompatible ChimeraX

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Updates

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/lewisj/Library/Application Support/ChimeraX/1.4/site-
packages  
sysconfig: /Users/lewisj/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/lewisj/Library/Application Support/ChimeraX/1.4/site-
packages  
sysconfig: /Users/lewisj/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/lewisj/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-ISOLDE  
sysconfig: /Users/lewisj/Library/Python/3.9/include/ChimeraX-ISOLDE  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/lewisj/Library/Application Support/ChimeraX/bin  
sysconfig: /Users/lewisj/Library/Python/3.9/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/lewisj/Library/Application Support/ChimeraX  
sysconfig: /Users/lewisj/Library/Python/3.9  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/lewisj/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /Users/lewisj/Library/Python/3.9/include/UNKNOWN  
WARNING: You are using pip version 21.3.1; however, version 22.1.2 is
available.  
You should consider upgrading via the
'/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -m pip
install --upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Collecting ChimeraX-ISOLDE==1.3  
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxisolde/releases/1.3/ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl
(81.8 MB)  
Installing collected packages: ChimeraX-ISOLDE  
Successfully installed ChimeraX-ISOLDE-1.3  
\---  

Successfully installed ChimeraX-ISOLDE-1.3  
Installed ChimeraX-ISOLDE (1.3)  

Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py",
line 127, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>  
__version__ = _version()  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 891, in require  
needed = self.resolve(parse_requirements(requirements))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 782, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 7.0
(/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX-
ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize  
api = self._get_api(session.logger)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api  
m = self.get_module()  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 7.0
(/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX-
ISOLDE'})  
  

ChimeraX-ISOLDE (installed) [version: 1.3] [api package: chimerax.isolde]
[category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive
Molecular Dynamics Flexible Fitting (iMDFF)]] [command: isolde [categories:
General] [synopsis: Command-line control of ISOLDE simulations]] [command:
rama [categories: General] [synopsis: Live Ramachandran validation of models]]
[command: rota [categories: General] [synopsis: Live rotamer validation of
models]] [command: ~rama [categories: General] [synopsis: Turn off live
Ramachandran validation of models]] [command: ~rota [categories: General]
[synopsis: Turn off live rotamer validation of models]]: custom initialization
failed  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

[Repeated 1 time(s)]

> ui tool show ISOLDE

Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py",
line 127, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>  
__version__ = _version()  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 891, in require  
needed = self.resolve(parse_requirements(requirements))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 782, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 7.0
(/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX-
ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 558, in start_tool  
api = self._get_api(session.logger)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api  
m = self.get_module()  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 7.0
(/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX-
ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1685, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.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
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.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
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 564, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-AtomicLibrary 7.0
(/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX-
ISOLDE'})  
  

Populating font family aliases took 327 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-AtomicLibrary 7.0
(/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX-
ISOLDE'})  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 564, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-18.7.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
      OS Loader Version: 540.120.3~6

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 11 days 21:05

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        BenQ EW2780:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: B9K0272101Q 
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 0.00


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Tom Goddard]

I think I reported this same problem before.

Toolshed seems to be broken offering to install ISOLDE 1.3 in ChimeraX 1.4 which does not have a compatible atomic library (needs 4.2, but ChimeraX 1.4 has 7.0). If I recall the explanation was that Toolshed only checks if the ChimeraX core requirement is satisfied when it decides to show the Install button on the Toolshed page. And ISOLDE 1.3 has core~=1.3rc2021... as a requirement so that matches 1.4.

Given this deficiency in Toolshed it might be wise to release an ISOLDE 1.3.1 that has core~=1.3.0 (or whatever is the magic to say 1.3 only).

I'm surprised we have not seen loads of these bug reports. How would a ChimeraX 1.4 user know that that ISOLDE 1.3 won't work on 1.4? Maybe they just don't bother to report this error?

Greg is on vacation for 3 weeks.

[Greg Couch]

I've patched this by hand by changing the dependency shown by the toolshed. But it would be better if there were a bug fix release with the fixed dependency. To do it by hand, a toolshed admin, basically the core ChimeraX developers, can use the admin interface to edit the dependency. The URL is the toolshed/admin, but be sure to login via the normal toolshed site first. Then click on Releases, then find the bundle (in the ISOLDE case, there 3, one for each platform). Click on the bundle name (not the check box). Then edit the "Works With" field to be "(~=1.3.0)". And then click the blue Save button in the lower right-hand corner. (Repeat for the other platforms.)

[Eric Pettersen]

The problem isn't the dependency on core ~= 1.3. There is nothing in the 1.4 core that breaks ISOLDE. The problem is that the toolshed only checks the core dependency. ISOLDE properly declares a dependency on AtomicLib 4.2 and the 1.4 release has AtomicLib 7.0. The toolshed should check the compatibility of all the dependencies.

Nonetheless, we already have a ticket for this (#6400), so no reason to keep this one open.