Opened 5 years ago

Last modified 5 years ago

#4562 assigned defect

Clipper not found

Reported by: dgil@… 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-4.12.14-lp151.28.52-default-x86_64-with-glibc2.14
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open Runs/018585_ProtRelionClassify3D/extra/chimera_volumes.cxc

> open relion_it050_class001.mrc

Opened relion_it050_class001.mrc, grid size 226,226,226, pixel 2.13, shown at
level 0.0126, step 1, values float32  

> open relion_it050_class002.mrc

Opened relion_it050_class002.mrc, grid size 226,226,226, pixel 2.13, shown at
level 0.0127, step 1, values float32  

> open relion_it050_class003.mrc

Opened relion_it050_class003.mrc, grid size 226,226,226, pixel 2.13, shown at
level 0.0126, step 1, values float32  

> open relion_it050_class004.mrc

Opened relion_it050_class004.mrc, grid size 226,226,226, pixel 2.13, shown at
level 0.0128, step 1, values float32  

> open relion_it050_class005.mrc

Opened relion_it050_class005.mrc, grid size 226,226,226, pixel 2.13, shown at
level 0.0127, step 1, values float32  

> open relion_it050_class006.mrc

Opened relion_it050_class006.mrc, grid size 226,226,226, pixel 2.13, shown at
level 0.0126, step 1, values float32  

> open relion_it050_class007.mrc

Opened relion_it050_class007.mrc, grid size 226,226,226, pixel 2.13, shown at
level 0.0126, step 1, values float32  

> open relion_it050_class008.mrc

Opened relion_it050_class008.mrc, grid size 226,226,226, pixel 2.13, shown at
level 0.0126, step 1, values float32  

> tile

8 models tiled  
executed chimera_volumes.cxc  
Successfully installed ChimeraX-ISOLDE-1.1.0  
Installed ChimeraX-ISOLDE (1.1.0)  

Traceback (most recent call last):  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/importlib/__init__.py",
line 127, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import  
File "<frozen importlib._bootstrap>", line 983, in _find_and_load  
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 728, in exec_module  
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed  
File "/home/virus/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 41, in <module>  
__version__ = _version()  
File "/home/virus/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 39, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 899, in require  
needed = self.resolve(parse_requirements(requirements))  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 785, in resolve  
raise DistributionNotFound(req, requirers)  
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.15.0'
distribution was not found and is required by ChimeraX-ISOLDE  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 341, in initialize  
api = self._get_api(session.logger)  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 454, 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: The 'ChimeraX-Clipper~=0.15.0' distribution was not found and is
required by ChimeraX-ISOLDE  
  

ChimeraX-ISOLDE (installed) [version: 1.1.0] [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  

Successfully installed ChimeraX-ISOLDE-1.1.0  
Installed ChimeraX-ISOLDE (1.1.0)  

Traceback (most recent call last):  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 452, in get_module  
m = importlib.import_module(self.package_name)  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/importlib/__init__.py",
line 127, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import  
File "<frozen importlib._bootstrap>", line 983, in _find_and_load  
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 728, in exec_module  
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed  
File "/home/virus/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 41, in <module>  
__version__ = _version()  
File "/home/virus/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 39, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 899, in require  
needed = self.resolve(parse_requirements(requirements))  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 785, in resolve  
raise DistributionNotFound(req, requirers)  
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.15.0'
distribution was not found and is required by ChimeraX-ISOLDE  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 341, in initialize  
api = self._get_api(session.logger)  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 478, in _get_api  
m = self.get_module()  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 454, 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: The 'ChimeraX-Clipper~=0.15.0' distribution was not found and is
required by ChimeraX-ISOLDE  
  

ChimeraX-ISOLDE (installed) [version: 1.1.0] [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  

Traceback (most recent call last):  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 223, in install  
self.cancel()  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 115, in cancel  
self.session.ui.main_window.close_request(self.tool_window)  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.toolshed_utils.tool.UpdateTool object at 0x7f1fee62a0d0>  
  
KeyError:  
  
File
"/home/virus/SOFTWARE/SCIPION/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 450.57
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: WS-C621E-SAGE Series
OS: openSUSE Leap 15.1 
Architecture: 64bit ELF
CPU: 80 Intel(R) Xeon(R) Gold 6230 CPU @ 2.10GHz
Cache Size: 28160 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          754Gi        45Gi       2.6Gi       261Mi       706Gi       704Gi
	Swap:         2.0Gi       788Mi       1.2Gi

Graphics:
	02:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:86ed]	
	Kernel driver in use: ast
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (3)

comment:1 by Eric Pettersen, 5 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 → Clipper not found

in reply to:  2 ; comment:2 by Tristan Croll, 5 years ago 

Hmm... haven't seen anything like that for a while. I notice this is the same session in which you actually installed ISOLDE. Normally that shouldn't be a problem... but can you try restarting ChimeraX and see if that helps?
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 26 April 2021 17:37
Cc: dgil@cnb.csic.es <dgil@cnb.csic.es>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4562: Clipper not found (was: ChimeraX bug report submission)

#4562: Clipper not found
--------------------------------+------------------------
          Reporter:  dgil@…     |      Owner:  Greg Couch
              Type:  defect     |     Status:  assigned
          Priority:  normal     |  Milestone:
         Component:  Tool Shed  |    Version:
        Resolution:             |   Keywords:
        Blocked By:             |   Blocking:
Notify when closed:             |   Platform:  all
           Project:  ChimeraX   |
--------------------------------+------------------------
Changes (by Eric Pettersen):

 * status:  new => assigned
 * cc: Tristan Croll (added)
 * component:  Unassigned => Tool Shed
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Greg Couch


--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4562#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  3 ; comment:3 by dgil@…, 5 years ago 

Hi, this was trying to install from the pop up that did appear just  
after starting ChimeraX (where different things can be installed).  
Afterwards, I followed the step from isolde instruction, where the  
installation is made differently and it was installed fine, apparently.



Quoting ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>:
Note: See TracTickets for help on using tickets.