Opened 4 years ago

Last modified 4 years ago

#5940 feedback defect

SMILES server-connection failure

Reported by: cyeow1@… Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Build Structure will not work when generating structure through SMILES. This problem occurs in Chimera 1.16 as well.

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  

> ui tool show "Build Structure"

Updating list of available bundles failed: Service Unavailable  

> open O=C1C2=CC=CC(N)=C2NC3=C1C=C(F)C=N3 fromDatabase smiles

Traceback (most recent call last):  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\build_structure\tool.py", line 294, in <lambda>  
apply_but.clicked.connect(lambda checked: self._ss_apply_cb())  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\build_structure\tool.py", line 436, in _ss_apply_cb  
run(self.session, subcmd_string)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 150, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 421, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\smiles\\__init__.py", line 25, in fetch  
return smiles.fetch_smiles(session, ident, ignore_cache=ignore_cache)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\smiles\smiles.py", line 39, in fetch_smiles  
path = fetcher(session, smiles_string, web_smiles)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\smiles\smiles.py", line 64, in _cactus_fetch  
reply = open_input("http://%s/cgi-
bin/translate.tcl?smiles=%s&format=sdf&astyle=kekule"  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\io\io.py", line 36, in open_input  
result = urlopen(source)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
222, in urlopen  
return opener.open(url, data, timeout)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
525, in open  
response = self._open(req, data)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
542, in _open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
502, in _call_chain  
result = func(*args)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
1383, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
1358, in do_open  
r = h.getresponse()  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\http\client.py", line
1347, in getresponse  
response.begin()  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\http\client.py", line 307,
in begin  
version, status, reason = self._read_status()  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\http\client.py", line 268,
in _read_status  
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\socket.py", line 669, in
readinto  
return self._sock.recv_into(b)  
TimeoutError: [WinError 10060] A connection attempt failed because the
connected party did not properly respond after a period of time, or
established connection failed because connected host has failed to respond  
  
TimeoutError: [WinError 10060] A connection attempt failed because the
connected party did not properly respond after a period of time, or
established connection failed because connected host has failed to respond  
  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\socket.py", line 669, in
readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  

> open O=C1C2=CC=CC(N)=C2NC3=C1C=C(F)C=N3 fromDatabase smiles

Traceback (most recent call last):  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\build_structure\tool.py", line 294, in <lambda>  
apply_but.clicked.connect(lambda checked: self._ss_apply_cb())  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\build_structure\tool.py", line 436, in _ss_apply_cb  
run(self.session, subcmd_string)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 150, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 421, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\smiles\\__init__.py", line 25, in fetch  
return smiles.fetch_smiles(session, ident, ignore_cache=ignore_cache)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\smiles\smiles.py", line 39, in fetch_smiles  
path = fetcher(session, smiles_string, web_smiles)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\smiles\smiles.py", line 64, in _cactus_fetch  
reply = open_input("http://%s/cgi-
bin/translate.tcl?smiles=%s&format=sdf&astyle=kekule"  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\io\io.py", line 36, in open_input  
result = urlopen(source)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
222, in urlopen  
return opener.open(url, data, timeout)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
525, in open  
response = self._open(req, data)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
542, in _open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
502, in _call_chain  
result = func(*args)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
1383, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
1358, in do_open  
r = h.getresponse()  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\http\client.py", line
1347, in getresponse  
response.begin()  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\http\client.py", line 307,
in begin  
version, status, reason = self._read_status()  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\http\client.py", line 268,
in _read_status  
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\socket.py", line 669, in
readinto  
return self._sock.recv_into(b)  
TimeoutError: [WinError 10060] A connection attempt failed because the
connected party did not properly respond after a period of time, or
established connection failed because connected host has failed to respond  
  
TimeoutError: [WinError 10060] A connection attempt failed because the
connected party did not properly respond after a period of time, or
established connection failed because connected host has failed to respond  
  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\socket.py", line 669, in
readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  

> open O=C1C2=CC=CC(N)=C2NC3=C1C=C(F)C=N3 fromDatabase smiles

Traceback (most recent call last):  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\build_structure\tool.py", line 294, in <lambda>  
apply_but.clicked.connect(lambda checked: self._ss_apply_cb())  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\build_structure\tool.py", line 436, in _ss_apply_cb  
run(self.session, subcmd_string)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 150, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 421, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\smiles\\__init__.py", line 25, in fetch  
return smiles.fetch_smiles(session, ident, ignore_cache=ignore_cache)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\smiles\smiles.py", line 39, in fetch_smiles  
path = fetcher(session, smiles_string, web_smiles)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\smiles\smiles.py", line 64, in _cactus_fetch  
reply = open_input("http://%s/cgi-
bin/translate.tcl?smiles=%s&format=sdf&astyle=kekule"  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\io\io.py", line 36, in open_input  
result = urlopen(source)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
222, in urlopen  
return opener.open(url, data, timeout)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
525, in open  
response = self._open(req, data)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
542, in _open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
502, in _call_chain  
result = func(*args)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
1383, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\urllib\request.py", line
1358, in do_open  
r = h.getresponse()  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\http\client.py", line
1347, in getresponse  
response.begin()  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\http\client.py", line 307,
in begin  
version, status, reason = self._read_status()  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\http\client.py", line 268,
in _read_status  
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\socket.py", line 669, in
readinto  
return self._sock.recv_into(b)  
TimeoutError: [WinError 10060] A connection attempt failed because the
connected party did not properly respond after a period of time, or
established connection failed because connected host has failed to respond  
  
TimeoutError: [WinError 10060] A connection attempt failed because the
connected party did not properly respond after a period of time, or
established connection failed because connected host has failed to respond  
  
File "C:\Program Files (86x)\ChimeraX 1.2.5\bin\lib\socket.py", line 669, in
readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.5058
OpenGL renderer: Intel(R) HD Graphics 4600
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 10AAS1BJ00
OS: Microsoft Windows 10 Pro (Build 17763)
Memory: 17,064,996,864
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-4570T CPU @ 2.90GHz
OSLanguage: en-US
Locale: ('en_AU', '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: 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-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
    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
    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
    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
    pywin32: 228
    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: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → SMILES server-connection failure

comment:2 by pett, 4 years ago

Status: accepted → feedback

Hi Colleen,

Thanks for reporting this problem. Your SMILES string works for me, so could you try again? ChimeraX and Chimera convert SMILES strings into structures by contacting a server at the NIH, so if your site had temporary network problems connecting to the NIH web site, it is possible that trying again now would work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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