Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6177 closed defect (duplicate)

Timeout connecting to Modeller web service

Reported by: bowman.alex34@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.13.0-28-generic-x86_64-with-glibc2.34
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 /home/mplinux/BOWMAN_ALEX/MAO_Docking/Base_Files/7rt0.pdb format pdb

7rt0.pdb title:  
1.80 A resolution structure of mao from P. Nicotinovorans In complex with fad
[more info...]  
  
Chain information for 7rt0.pdb #1  
---  
Chain | Description | UniProt  
A | γ-N-methylaminobutyrate oxidase 2 | MABO2_PAENI  
  
Non-standard residues in 7rt0.pdb #1  
---  
FAD — flavin-adenine dinucleotide  
PG4 — tetraethylene glycol  
  

> open /home/mplinux/BOWMAN_ALEX/MAO_Docking/Base_Files/MAO_refine_14.pdb

Summary of feedback from opening
/home/mplinux/BOWMAN_ALEX/MAO_Docking/Base_Files/MAO_refine_14.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2017-01-24 Time 12:21:46 CST -0600 (1485282106.39 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/home/swlovell/structures/Richter_Mark/MAO/ccp4/MAO_Native_xdsapp_scaled1.mtz  
  
64 messages similar to the above omitted  
  
Chain information for MAO_refine_14.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select

8380 atoms, 8192 bonds, 5 pseudobonds, 1032 residues, 4 models selected  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7rt0.pdb, chain A (#1) with MAO_refine_14.pdb, chain A (#2),
sequence alignment score = 1343.2  
RMSD between 246 pruned atom pairs is 0.733 angstroms; (across all 336 pairs:
3.678)  
  

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7rt0.pdb, chain A (#1) with MAO_refine_14.pdb, chain A (#2),
sequence alignment score = 1343.2  
RMSD between 246 pruned atom pairs is 0.733 angstroms; (across all 336 pairs:
3.678)  
  

> ui tool show "Model Loops"

> ui tool show "Modeller Comparative"

> ui tool show Matchmaker

> matchmaker #!2 to #1 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7rt0.pdb, chain A (#1) with MAO_refine_14.pdb, chain A (#2),
sequence alignment score = 1343.2  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 7rt0.pdb #1/A,
MAO_refine_14.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 246 pruned atom pairs is 0.733 angstroms; (across all 336 pairs:
3.678)  
  

> matchmaker #!2 to #1 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7rt0.pdb, chain A (#1) with MAO_refine_14.pdb, chain A (#2),
sequence alignment score = 1343.2  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 7rt0.pdb #1/A,
MAO_refine_14.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 246 pruned atom pairs is 0.733 angstroms; (across all 336 pairs:
3.678)  
  

> ui tool show "Model Loops"

> modeller refine 2:1:internal-missing numModels 5 fast true adjacentFlexible
> 1 protocol standard

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1346, in
do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1257, in
request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1303, in
_send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1252, in
endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1012, in
_send_output  
self.send(msg)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 952, in send  
self.connect()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 923, in
connect  
self.sock = self._create_connection(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/socket.py", line 843, in
create_connection  
raise err  
File "/usr/lib/ucsf-chimerax/lib/python3.9/socket.py", line 831, in
create_connection  
sock.connect(sa)  
socket.timeout: timed out  
  
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/core/tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/suds/client.py", line
115, in __init__  
self.wsdl = reader.open(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/suds/reader.py", line
150, in open  
d = self.fn(url, self.options)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/suds/wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/suds/reader.py", line
74, in open  
d = self.download(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/suds/reader.py", line
92, in download  
fp = self.options.transport.open(Request(url))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/suds/transport/https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/suds/transport/http.py", line 67, in open  
return self.u2open(u2request)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/suds/transport/http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 517, in
open  
response = self._open(req, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 534, in
_open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 494, in
_call_chain  
result = func(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1375, in
http_open  
return self.do_open(http.client.HTTPConnection, req)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1349, in
do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error timed out>  
  
Exception in thread 1:  
urllib.error.URLError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1349, in
do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> ui tool show "Build Structure"

[Repeated 1 time(s)]

> ui tool show "Model Loops"

> modeller refine 2:1:internal-missing numModels 5 fast false adjacentFlexible
> 1 protocol standard

> ui tool show AlphaFold

> ui tool show "Build Structure"

> select clear

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1346, in
do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1257, in
request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1303, in
_send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1252, in
endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1012, in
_send_output  
self.send(msg)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 952, in send  
self.connect()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 923, in
connect  
self.sock = self._create_connection(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/socket.py", line 843, in
create_connection  
raise err  
File "/usr/lib/ucsf-chimerax/lib/python3.9/socket.py", line 831, in
create_connection  
sock.connect(sa)  
socket.timeout: timed out  
  
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/core/tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/suds/client.py", line
115, in __init__  
self.wsdl = reader.open(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/suds/reader.py", line
150, in open  
d = self.fn(url, self.options)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/suds/wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/suds/reader.py", line
74, in open  
d = self.download(url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/suds/reader.py", line
92, in download  
fp = self.options.transport.open(Request(url))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/suds/transport/https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/suds/transport/http.py", line 67, in open  
return self.u2open(u2request)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/suds/transport/http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 517, in
open  
response = self._open(req, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 534, in
_open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 494, in
_call_chain  
result = func(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1375, in
http_open  
return self.do_open(http.client.HTTPConnection, req)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1349, in
do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error timed out>  
  
Exception in thread 2:  
urllib.error.URLError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1349, in
do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/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 "/usr/lib/ucsf-chimerax/lib/python3.9/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 510.39.01
OpenGL renderer: NVIDIA GeForce RTX 3080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 21.10 impish
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen 9 5950X 16-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       3.7Gi        56Gi       112Mi       2.8Gi        58Gi
	Swap:           93Gi          0B        93Gi

Graphics:
	09:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3080 Ti] [10de:2208] (rev a1)	
	Subsystem: eVga.com. Corp. GA102 [GeForce RTX 3080 Ti] [3842:3967]	
	Kernel driver in use: nvidia
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: 21.2.4
    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

Change History (5)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Timeout connecting to Modeller web service

comment:2 by Eric Pettersen, 4 years ago

Status: accepted → feedback

Hi Alex,

I am having no trouble running Modeller from ChimeraX, so perhaps this was some kind of temporary networking problem between your site and our web servers. Could you try again and let me know if you are continuing to experience this problem?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Eric Pettersen, 4 years ago

Resolution: → duplicate
Status: feedback → closed

I see this issue is being handled in ticket #6178.

in reply to:  4 ; comment:4 by bowman.alex34@…, 4 years ago 

Hi Eric,

Sorry for the late reply - I will try to run it again right now. Thanks to everyone for looking into this!

Alex Bowman

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, February 15, 2022 7:37 PM
To: undisclosed-recipients:
Cc: bowman.alex34@gmail.com; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #6177: Timeout connecting to Modeller web service

#6177: Timeout connecting to Modeller web service
--------------------------------------+----------------------
          Reporter:  bowman.alex34@…  |      Owner:  pett
              Type:  defect           |     Status:  feedback
          Priority:  normal           |  Milestone:
         Component:  Sequence         |    Version:
        Resolution:                   |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 Hi Alex,
         I am having no trouble running Modeller from ChimeraX, so perhaps  this was some kind of temporary networking problem between your site and  our web servers.  Could you try again and let me know if you are  continuing to experience this problem?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6177#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:5 by Eric Pettersen, 4 years ago

It turns out that the UCSF campus firewall was blocking the port needed to reach the Modeller service. That has been resolved now, so I would expect things to work for you.

--Eric

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