id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6177 Timeout connecting to Modeller web service bowman.alex34@… Eric Pettersen "{{{ 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: 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: 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 }}} " defect closed normal Sequence duplicate all ChimeraX