Opened 4 years ago

Closed 4 years ago

#5596 closed defect (can't reproduce)

Modeller comparative: HTTP Error 403: Forbidden

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.11.0-38-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> show # target m

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> fetch

Unknown command: fetch  

> open /home/davide/Desktop/all-atom/DDX19/close/3g0h.pdb

3g0h.pdb title:  
Human dead-box RNA helicase DDX19, In complex with an atp-analogue and RNA
[more info...]  
  
Chain information for 3g0h.pdb #1  
---  
Chain | Description  
A | atp-dependent RNA helicase DDX19B  
E | 5'-R(P*up*up*up*up*up*up*U)-3'  
  
Non-standard residues in 3g0h.pdb #1  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
  

> ui tool show "Blast Protein"

> select ::name="ANP"::name="GOL"::name="MG"

38 atoms, 38 bonds, 2 pseudobonds, 3 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service16367354055481416323877  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16367354055481416323877  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

> view #1 clip false

Alignment identifier is bp1 [1]  
Associated 3g0h.pdb chain A to 3EWS_A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]  

> select /A:60-467

3225 atoms, 3279 bonds, 408 residues, 1 model selected  

> ui tool show "Modeller Comparative"

No target sequence chosen for alignment bp1 [1]  

> modeller comparative "bp1 [1]:1" multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service16367355850791069640172  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16367355850791069640172  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service16367355850791069640172 finished  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 648, in customEvent  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/modeller/comparative.py", line 478, in on_finish  
self.caller.process_ok_models(model_info, stdout, get_pdb_model)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/modeller/common.py", line 314, in process_ok_models  
model = get_pdb_model(pdb_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/modeller/comparative.py", line 473, in get_pdb_model  
pdb_text = self.get_file(fname)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/webservices/opal_job.py", line 267, in get_file  
with urlopen(url) as f:  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 222, in
urlopen  
return opener.open(url, data, timeout)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 531, in
open  
response = meth(req, response)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 640, in
http_response  
response = self.parent.error(  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 569, in
error  
return self._call_chain(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 502, in
_call_chain  
result = func(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 403: Forbidden  
  
urllib.error.HTTPError: HTTP Error 403: Forbidden  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
  
See log for complete Python traceback.  
  

> ui tool show "Modeller Comparative"

> modeller comparative "bp1 [1]:1" multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service16367357403941388999235  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16367357403941388999235  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service16367357403941388999235 finished  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 648, in customEvent  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/modeller/comparative.py", line 478, in on_finish  
self.caller.process_ok_models(model_info, stdout, get_pdb_model)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/modeller/common.py", line 314, in process_ok_models  
model = get_pdb_model(pdb_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/modeller/comparative.py", line 473, in get_pdb_model  
pdb_text = self.get_file(fname)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/webservices/opal_job.py", line 267, in get_file  
with urlopen(url) as f:  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 222, in
urlopen  
return opener.open(url, data, timeout)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 531, in
open  
response = meth(req, response)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 640, in
http_response  
response = self.parent.error(  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 569, in
error  
return self._call_chain(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 502, in
_call_chain  
result = func(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 403: Forbidden  
  
urllib.error.HTTPError: HTTP Error 403: Forbidden  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.3 (Core Profile) Mesa 21.0.3
OpenGL renderer: NVE7
OpenGL vendor: nouveau
Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v4 @ 3.60GHz
Cache Size: 15360 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       5.5Gi       221Mi       339Mi       9.8Gi       9.4Gi
	Swap:         486Mi       7.0Mi       479Mi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK107GL [Quadro K420] [10de:0ff3] (rev a1)	
	Subsystem: NVIDIA Corporation GK107GL [Quadro K420] [10de:1162]	
	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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Structure Prediction
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Modeller comparative: HTTP Error 403: Forbidden

comment:2 by pett, 4 years ago

Resolution: → can't reproduce
Status: accepted → closed
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