Opened 3 years ago

Last modified 3 years ago

#7803 assigned defect

Install ISOLDE into ChimeraX 1.5

Reported by: roger.b.sutton@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Tristan Croll
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-50-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.5rc202210140205 (2022-10-14 02:05:18 UTC)
Description
Tried to install ISODE on a fresh install of chimerax. Using Ubuntu 22.10

Log:
UCSF ChimeraX version: 1.5rc202210140205 (2022-10-14)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Updates

Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-ArtiaX-0.3 ChimeraX-
Clipper-0.18.0 ChimeraX-Cytoscape-0.1 ChimeraX-DevelExtras-0.4.2 ChimeraX-
GenomeTools-0.9 ChimeraX-HKCage-1.3 ChimeraX-ISOLDE-1.4 ChimeraX-
NIHPresets-1.1 ChimeraX-PDBImages-1.1 ChimeraX-Phenix-0.3 ChimeraX-
PhenixUI-1.0.5 ChimeraX-RIBFIND-0.2 ChimeraX-RMF-0.11 ChimeraX-TestManager-0.3
ChimeraX-UI-1.2.1 ChimeraX-XMAS-1.1.2 MolecularDynamicsViewer-1.4
SEQCROW-1.5.4  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-ArtiaX (0.3)  
Installed ChimeraX-Clipper (0.18.0)  
Installed ChimeraX-Cytoscape (0.1)  
Installed ChimeraX-DevelExtras (0.4.2)  
Installed ChimeraX-GenomeTools (0.9)  
Installed ChimeraX-HKCage (1.3)  
Installed ChimeraX-ISOLDE (1.4)  
Installed ChimeraX-NIHPresets (1.1)  
Installed ChimeraX-PDBImages (1.1)  
Installed ChimeraX-Phenix (0.3)  
Installed ChimeraX-PhenixUI (1.0.5)  
Installed ChimeraX-RIBFIND (0.2)  
Installed ChimeraX-RMF (0.11)  
Installed ChimeraX-TestManager (0.3)  
Installed ChimeraX-UI (1.2.1)  
Installed ChimeraX-XMAS (1.1.2)  
Installed MolecularDynamicsViewer (1.4)  
Installed SEQCROW (1.5.4)  

Unable to find icon for toolbar provider 'Dump Bead Data' in bundle 'ChimeraX-
GenomeTools'  

Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'  

Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'  

Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'  

Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'  

Unable to find icon for toolbar provider 'Genome Selection' in bundle
'ChimeraX-GenomeTools'  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
File "/usr/lib/ucsf-chimerax/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 "/home/rosutton/.local/share/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>  
__version__ = _version()  
File "/home/rosutton/.local/share/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 909, in require  
needed = self.resolve(parse_requirements(requirements))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 800, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 8.0.2
(/usr/lib/ucsf-chimerax/lib/python3.9/site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=7.0'), {'ChimeraX-ISOLDE',
'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize  
api = self._get_api(session.logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api  
m = self.get_module()  
File "/usr/lib/ucsf-chimerax/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 8.0.2 (/usr/lib/ucsf-
chimerax/lib/python3.9/site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=7.0'), {'ChimeraX-ISOLDE', 'ChimeraX-Clipper'})  
  

ChimeraX-ISOLDE (installed) [version: 1.4] [api package: chimerax.isolde]
[category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive
Molecular Dynamics Flexible Fitting (iMDFF)]] [tool: Ramachandran Plot
[categories: Validation] [synopsis: Interactive Ramachandran plot]] [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  

> ui tool show ISOLDE

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
File "/usr/lib/ucsf-chimerax/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 "/home/rosutton/.local/share/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>  
__version__ = _version()  
File "/home/rosutton/.local/share/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 909, in require  
needed = self.resolve(parse_requirements(requirements))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 800, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 8.0.2
(/usr/lib/ucsf-chimerax/lib/python3.9/site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=7.0'), {'ChimeraX-ISOLDE',
'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
api = self._get_api(session.logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api  
m = self.get_module()  
File "/usr/lib/ucsf-chimerax/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 8.0.2 (/usr/lib/ucsf-
chimerax/lib/python3.9/site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=7.0'), {'ChimeraX-ISOLDE', 'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1660, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/cmd.py",
line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 567, 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 8.0.2
(/usr/lib/ucsf-chimerax/lib/python3.9/site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=7.0'), {'ChimeraX-ISOLDE',
'ChimeraX-Clipper'})  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-AtomicLibrary 8.0.2
(/usr/lib/ucsf-chimerax/lib/python3.9/site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=7.0'), {'ChimeraX-ISOLDE',
'ChimeraX-Clipper'})  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 567, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 515.65.01
OpenGL renderer: NVIDIA GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7C37
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 3900X 12-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       4.9Gi        43Gi        42Mi        14Gi        57Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	23:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP107GL [Quadro P1000] [10de:1cb1] (rev a1)	
	Subsystem: Dell GP107GL [Quadro P1000] [1028:11bc]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.0.8
    Babel: 2.10.3
    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: 2.1.3
    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-ArtiaX: 0.3
    ChimeraX-Atomic: 1.41.4
    ChimeraX-AtomicLibrary: 8.0.2
    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: 0.18.0
    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: 1.5rc202210140205
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-Cytoscape: 0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-DevelExtras: 0.4.2
    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-GenomeTools: 0.9
    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: 1.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.1
    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-NIHPresets: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PhenixUI: 1.0.5
    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-RIBFIND: 0.2
    ChimeraX-RMF: 0.11
    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-TestManager: 0.3
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.2.1
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    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-XMAS: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.1
    filelock: 3.7.1
    fonttools: 4.37.4
    funcparserlib: 1.0.0
    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: 5.0.0
    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: 4.11.1
    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
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.3
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    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: 2022.4
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    SEQCROW: 1.5.4
    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: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.9.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tristan Croll added
Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Install ISOLDE into ChimeraX 1.5

Reported by Bryan Sutton

in reply to:  2 ; comment:2 by Tristan Croll, 3 years ago 

I tracked down the reason behind this - ultimately a misunderstanding on my
part. Amazingly, according to the relevant PEP “~=1.4.dev1233” is
equivalent to “>=1.4.dev1234, <2.0”, not “>=1.4.dev1234, <1.5”. Will fix in
the next release.

On Mon, 17 Oct 2022 at 18:41, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:
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