Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#8230 closed defect (limitation)

Wiggle tool not found after installation

Reported by: makaia@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Tom Goddard, Charles.Bayly-Jones@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-56-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> devel build /home/makaia/wiggle/wiggle/

running build  
running build_py  
running bdist_wheel  
installing to build/bdist.linux-x86_64/wheel  
running install  
running install_lib  
creating build/bdist.linux-x86_64/wheel  
creating build/bdist.linux-x86_64/wheel/chimerax  
creating build/bdist.linux-x86_64/wheel/chimerax/wiggle  
copying build/lib/chimerax/wiggle/tool.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle  
creating build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/low_pass.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/miniDRGN.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/dijkstra_modified.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
creating build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps/__pycache__  
copying build/lib/chimerax/wiggle/deps/__pycache__/ui_compiled.cpython-37.pyc
-> build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps/__pycache__  
copying build/lib/chimerax/wiggle/deps/volumiser.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/clustering.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/wiggle_packager.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/data_handler.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/path_inference_dijkstra.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/mrc.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/embedding.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/ui_compiled.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/miniSPARC.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
creating build/bdist.linux-x86_64/wheel/chimerax/wiggle/resources  
copying build/lib/chimerax/wiggle/resources/Wiggle2.PNG ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/resources  
copying build/lib/chimerax/wiggle/resources/Wiggle.PNG ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/resources  
copying build/lib/chimerax/wiggle/wiggle.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle  
copying build/lib/chimerax/wiggle/__init__.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle  
running install_egg_info  
running egg_info  
writing wiggle.egg-info/PKG-INFO  
writing dependency_links to wiggle.egg-info/dependency_links.txt  
writing requirements to wiggle.egg-info/requires.txt  
writing top-level names to wiggle.egg-info/top_level.txt  
reading manifest file 'wiggle.egg-info/SOURCES.txt'  
adding license file 'LICENSE'  
writing manifest file 'wiggle.egg-info/SOURCES.txt'  
Copying wiggle.egg-info to
build/bdist.linux-x86_64/wheel/wiggle-0.2.2-py3.9.egg-info  
running install_scripts  
adding license file "LICENSE" (matched pattern "LICEN[CS]E*")  
creating build/bdist.linux-x86_64/wheel/wiggle-0.2.2.dist-info/WHEEL  
creating 'dist/wiggle-0.2.2-py3-none-any.whl' and adding
'build/bdist.linux-x86_64/wheel' to it  
adding 'chimerax/wiggle/__init__.py'  
adding 'chimerax/wiggle/tool.py'  
adding 'chimerax/wiggle/wiggle.py'  
adding 'chimerax/wiggle/deps/clustering.py'  
adding 'chimerax/wiggle/deps/data_handler.py'  
adding 'chimerax/wiggle/deps/dijkstra_modified.py'  
adding 'chimerax/wiggle/deps/embedding.py'  
adding 'chimerax/wiggle/deps/low_pass.py'  
adding 'chimerax/wiggle/deps/miniDRGN.py'  
adding 'chimerax/wiggle/deps/miniSPARC.py'  
adding 'chimerax/wiggle/deps/mrc.py'  
adding 'chimerax/wiggle/deps/path_inference_dijkstra.py'  
adding 'chimerax/wiggle/deps/ui_compiled.py'  
adding 'chimerax/wiggle/deps/volumiser.py'  
adding 'chimerax/wiggle/deps/wiggle_packager.py'  
adding 'chimerax/wiggle/deps/__pycache__/ui_compiled.cpython-37.pyc'  
adding 'chimerax/wiggle/resources/Wiggle.PNG'  
adding 'chimerax/wiggle/resources/Wiggle2.PNG'  
adding 'wiggle-0.2.2.dist-info/LICENSE'  
adding 'wiggle-0.2.2.dist-info/METADATA'  
adding 'wiggle-0.2.2.dist-info/WHEEL'  
adding 'wiggle-0.2.2.dist-info/top_level.txt'  
adding 'wiggle-0.2.2.dist-info/RECORD'  
removing build/bdist.linux-x86_64/wheel  
Distribution is in /home/makaia/wiggle/wiggle/dist/wiggle-0.2.2-py3-none-
any.whl  
  

> devel install /home/makaia/wiggle/wiggle/

running build  
running build_py  
running bdist_wheel  
installing to build/bdist.linux-x86_64/wheel  
running install  
running install_lib  
creating build/bdist.linux-x86_64/wheel  
creating build/bdist.linux-x86_64/wheel/chimerax  
creating build/bdist.linux-x86_64/wheel/chimerax/wiggle  
copying build/lib/chimerax/wiggle/tool.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle  
creating build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/low_pass.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/miniDRGN.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/dijkstra_modified.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
creating build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps/__pycache__  
copying build/lib/chimerax/wiggle/deps/__pycache__/ui_compiled.cpython-37.pyc
-> build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps/__pycache__  
copying build/lib/chimerax/wiggle/deps/volumiser.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/clustering.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/wiggle_packager.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/data_handler.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/path_inference_dijkstra.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/mrc.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/embedding.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/ui_compiled.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
copying build/lib/chimerax/wiggle/deps/miniSPARC.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/deps  
creating build/bdist.linux-x86_64/wheel/chimerax/wiggle/resources  
copying build/lib/chimerax/wiggle/resources/Wiggle2.PNG ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/resources  
copying build/lib/chimerax/wiggle/resources/Wiggle.PNG ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle/resources  
copying build/lib/chimerax/wiggle/wiggle.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle  
copying build/lib/chimerax/wiggle/__init__.py ->
build/bdist.linux-x86_64/wheel/chimerax/wiggle  
running install_egg_info  
running egg_info  
writing wiggle.egg-info/PKG-INFO  
writing dependency_links to wiggle.egg-info/dependency_links.txt  
writing requirements to wiggle.egg-info/requires.txt  
writing top-level names to wiggle.egg-info/top_level.txt  
reading manifest file 'wiggle.egg-info/SOURCES.txt'  
adding license file 'LICENSE'  
writing manifest file 'wiggle.egg-info/SOURCES.txt'  
Copying wiggle.egg-info to
build/bdist.linux-x86_64/wheel/wiggle-0.2.2-py3.9.egg-info  
running install_scripts  
adding license file "LICENSE" (matched pattern "LICEN[CS]E*")  
creating build/bdist.linux-x86_64/wheel/wiggle-0.2.2.dist-info/WHEEL  
creating 'dist/wiggle-0.2.2-py3-none-any.whl' and adding
'build/bdist.linux-x86_64/wheel' to it  
adding 'chimerax/wiggle/__init__.py'  
adding 'chimerax/wiggle/tool.py'  
adding 'chimerax/wiggle/wiggle.py'  
adding 'chimerax/wiggle/deps/clustering.py'  
adding 'chimerax/wiggle/deps/data_handler.py'  
adding 'chimerax/wiggle/deps/dijkstra_modified.py'  
adding 'chimerax/wiggle/deps/embedding.py'  
adding 'chimerax/wiggle/deps/low_pass.py'  
adding 'chimerax/wiggle/deps/miniDRGN.py'  
adding 'chimerax/wiggle/deps/miniSPARC.py'  
adding 'chimerax/wiggle/deps/mrc.py'  
adding 'chimerax/wiggle/deps/path_inference_dijkstra.py'  
adding 'chimerax/wiggle/deps/ui_compiled.py'  
adding 'chimerax/wiggle/deps/volumiser.py'  
adding 'chimerax/wiggle/deps/wiggle_packager.py'  
adding 'chimerax/wiggle/deps/__pycache__/ui_compiled.cpython-37.pyc'  
adding 'chimerax/wiggle/resources/Wiggle.PNG'  
adding 'chimerax/wiggle/resources/Wiggle2.PNG'  
adding 'wiggle-0.2.2.dist-info/LICENSE'  
adding 'wiggle-0.2.2.dist-info/METADATA'  
adding 'wiggle-0.2.2.dist-info/WHEEL'  
adding 'wiggle-0.2.2.dist-info/top_level.txt'  
adding 'wiggle-0.2.2.dist-info/RECORD'  
removing build/bdist.linux-x86_64/wheel  
Distribution is in /home/makaia/wiggle/wiggle/dist/wiggle-0.2.2-py3-none-
any.whl  
[toolshed install](help:user/commands/toolshed.html#install)  
/home/makaia/wiggle/wiggle/dist/wiggle-0.2.2-py3-none-any.whl reinstall true  
  
[toolshed install /home/makaia/wiggle/wiggle/dist/wiggle-0.2.2-py3-none-  
any.whl reinstall true](cxcmd:toolshed install  
/home/makaia/wiggle/wiggle/dist/wiggle-0.2.2-py3-none-any.whl reinstall true)  
  
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: /home/makaia/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/makaia/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/makaia/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/makaia/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/makaia/.local/share/ChimeraX/include/python3.9/wiggle  
sysconfig: /home/makaia/.local/include/python3.9/wiggle  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/makaia/.local/share/ChimeraX/bin  
sysconfig: /home/makaia/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/makaia/.local/share/ChimeraX  
sysconfig: /home/makaia/.local  
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: /home/makaia/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/makaia/.local/include/python3.9/UNKNOWN  
\---  
pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./wiggle/wiggle/dist/wiggle-0.2.2-py3-none-any.whl  
Installing collected packages: wiggle  
Attempting uninstall: wiggle  
Found existing installation: wiggle 0.2.2  
Uninstalling wiggle-0.2.2:  
Successfully uninstalled wiggle-0.2.2  
Successfully installed wiggle-0.2.2  
\---  
Successfully installed wiggle-0.2.2  
Installed wiggle (0.2.2)  
  

> ui tool show wiggle

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 554, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1323, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "/home/makaia/.local/share/ChimeraX/1.3/site-
packages/chimerax/wiggle/__init__.py", line 31, in start_tool  
raise ValueError("trying to start unknown tool: %s" % ti.name)  
ValueError: trying to start unknown tool: wiggle  
  
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/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, 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 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool wiggle in
bundle wiggle:  
trying to start unknown tool: wiggle  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool wiggle in
bundle wiggle:  
trying to start unknown tool: wiggle  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show wiggle

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 554, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1323, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "/home/makaia/.local/share/ChimeraX/1.3/site-
packages/chimerax/wiggle/__init__.py", line 31, in start_tool  
raise ValueError("trying to start unknown tool: %s" % ti.name)  
ValueError: trying to start unknown tool: wiggle  
  
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/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, 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 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool wiggle in
bundle wiggle:  
trying to start unknown tool: wiggle  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool wiggle in
bundle wiggle:  
trying to start unknown tool: wiggle  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.3 (Core Profile) Mesa 21.2.6
OpenGL renderer: NV136
OpenGL vendor: nouveau
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7A38
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 AMD Ryzen 5 3600 6-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi       2.0Gi       1.8Gi        28Mi        27Gi        28Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	29:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP106 [GeForce GTX 1060 6GB] [10de:1c03] (rev a1)	
	Subsystem: NVIDIA Corporation GP106 [GeForce GTX 1060 6GB] [10de:11d7]	
	Kernel driver in use: nouveau
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 22.3.1
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    wiggle: 0.2.2

Change History (3)

comment:1 by pett, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Wiggle tool not found after installation

Reported by Makaía Papasergi-Scott

comment:2 by Greg Couch, 3 years ago

Resolution: → limitation
Status: assigned → closed

We had several bugs that prevented the Wiggle wheel (.whl file) from being installed correctly that we fixed in ChimeraX 1.5. Please upgrade ChimeraX and try again. If you still have problems, we'll dig deeper.

comment:3 by Tom Goddard, 3 years ago

Cc: Charles.Bayly-Jones@… added

It may be that you have to restart ChimeraX before the Wiggle menu entry will work. That would be a bug in ChimeraX.

The changes Greg mentioned to improve the install of Wiggle were to allow Wiggle to be installed along with the PyPi package it needs using the ChimeraX Toolshed (menu Tools / More Tools...) which would simplify the installation process. But Wiggle (​https://github.com/charbj/wiggle) has not been updated to install from the Toolshed. Updating Wiggle to install from the Toolshed is described in this ticket

​https://github.com/charbj/wiggle/issues/3

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