Timeout for Opal model-loops web service

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
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  

> open D:/p_bow_cu/moscatilin/5kcv/modeller/recep_5kcv.pdb

recep_5kcv.pdb title:  
Crystal structure of allosteric inhibitor, arq 092, In complex with
autoinhibited form of AKT1 [more info...]  
  
Chain information for recep_5kcv.pdb #1  
---  
Chain | Description | UniProt  
A | rac-α serine/threonine-protein kinase | AKT1_HUMAN  
  

> log metadata #1

Metadata for recep_5kcv.pdb #1  
---  
Title | Crystal structure of allosteric inhibitor, arq 092, In complex with
autoinhibited form of AKT1  
Citation | Discovery
OF3-(3-(4-(1-aminocyclobutyl)phenyl)-5-phenyl-3H-imidazo[4,5-B]pyridin-2-yl)pyridin-2-amine
(arq 092): an orallybioavailable, selective, and potent allosteric
aktinhibitor. PMID: 27305487  
Gene source | Homo sapiens (human)  
Experimental method | X-ray diffraction  
Resolution | 2.70Å  
Alignment identifier is 1/A  

> ui tool show "Model Loops"

> modeller refine 1/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard tempPath D:/p_bow_cu/moscatilin/5kcv/modeller/model

> ui tool show "Model Loops"

> modeller refine 1/A:1:all-missing numModels 5 fast true adjacentFlexible 1
> protocol standard tempPath D:/p_bow_cu/moscatilin/5kcv/modeller/model

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 555, in
error  
result = self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 747, in
http_error_302  
return self.parent.open(new, timeout=req.timeout)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 517, in
open  
response = self._open(req, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 534, in
_open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1389, in
https_open  
return self.do_open(http.client.HTTPSConnection, req,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1350, in
do_open  
r = h.getresponse()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1349, in
getresponse  
response.begin()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 316, in
begin  
version, status, reason = self._read_status()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 277, in
_read_status  
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\socket.py", line 704, in readinto  
return self._sock.recv_into(b)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1241, in recv_into  
return self.read(nbytes, buffer)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1099, in read  
return self._sslobj.read(len, buffer)  
socket.timeout: The read operation timed out  
  
Exception in thread 1:  
socket.timeout: The read operation timed out  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1099, in read  
return self._sslobj.read(len, buffer)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 516.01
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 17,084,624,896
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-US
Locale: ('th_TH', 'cp1252')
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-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
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    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
    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
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    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
    pywin32: 228
    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
    WMI: 1.5.1

[Eric Pettersen]

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