id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4782 Modeller: 'target_name' referenced before assignment blemire@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description Since installing version 1.2.5, I have been unable to successfully invoke modeller. Open an accession from UniProt. Run blast. Load top hit and show alignment. Invoke modeller using alignment with query aligned to top hit: Log file: open A0A1D8PU02 format uniprot fromDatabase uniprot Summary of feedback from opening A0A1D8PU02 fetched from uniprot note Alignment identifier is A0A1D8PU02 Opened UniProt A0A1D8PU02 blastprotein A0A1D8PU02:1Web 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: appBlastProtein2Service1623944771347941833351 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1623944771347941833351 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. open pdb:3JCM3jcm title: Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP [more info...] Chain information for 3jcm #1 Chain Description A Pre-mRNA-splicing factor 8 B U4/U6 small nuclear ribonucleoprotein PRP4 C pre-mRNA D SNR6 snRNA E SNR14 snRNA F SNR7-L snRNA G Pre-mRNA-splicing factor 6 H Pre-mRNA-splicing factor SNU114 I Pre-mRNA-processing factor 31 J R Small nuclear ribonucleoprotein Sm D3 K U4/U6 small nuclear ribonucleoprotein PRP3 L Spliceosomal protein DIB1 M 13 kDa ribonucleoprotein-associated protein N Pre-mRNA-splicing helicase BRR2 O S Small nuclear ribonucleoprotein-associated protein B P T Small nuclear ribonucleoprotein Sm D1 Q U Small nuclear ribonucleoprotein Sm D2 V Y Small nuclear ribonucleoprotein E W Z Small nuclear ribonucleoprotein F X a Small nuclear ribonucleoprotein G b U6 snRNA-associated Sm-like protein LSm8 c U6 snRNA-associated Sm-like protein LSm2 d U6 snRNA-associated Sm-like protein LSm3 e U6 snRNA-associated Sm-like protein LSm6 f U6 snRNA-associated Sm-like protein LSm5 g U6 snRNA-associated Sm-like protein LSm7 h U6 snRNA-associated Sm-like protein LSm4 Non-standard residues in 3jcm #1 GTP — guanosine-5'-triphosphate M7M — N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) select clearAlignment identifier is bp1 [1] Associated 3jcm chain B to 3JCM_B with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment bp1 [1] ui tool show ""Modeller Comparative""> has active key-value observers (KVO)! These will stop working now that the window is recreated, and will result in exceptions when the observers are removed. Break in QCocoaWindow::recreateWindowIfNeeded to debug. > has active key-value observers (KVO)! These will stop working now that the window is recreated, and will result in exceptions when the observers are removed. Break in QCocoaWindow::recreateWindowIfNeeded to debug. modeller comparative ""bp1 [1]:2"" multichain false numModels 5 fast false hetPreserve false hydrogens false tempPath /Users/blemire/Desktop/untitled_folder waterPreserve falseTraceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/modeller/tool.py"", line 140, in launch_modeller run(self.session, ""modeller comparative %s multichain %s numModels %d fast %s hetPreserve %s"" File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/modeller/cmd.py"", line 34, in sequence_model comparative.model(session, targets, block=block, multichain=multichain, File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/modeller/comparative.py"", line 215, in model pir_target = Sequence(name=opal_safe_file_name(target_name)) UnboundLocalError: local variable 'target_name' referenced before assignment UnboundLocalError: local variable 'target_name' referenced before assignment File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/modeller/comparative.py"", line 215, in model pir_target = Sequence(name=opal_safe_file_name(target_name)) See log for complete Python traceback. 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 > open A0A1D8PU02 format uniprot fromDatabase uniprot Summary of feedback from opening A0A1D8PU02 fetched from uniprot --- note | Alignment identifier is A0A1D8PU02 Opened UniProt A0A1D8PU02 > blastprotein A0A1D8PU02:1 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: appBlastProtein2Service1623944771347941833351 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1623944771347941833351 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. > open pdb:3JCM 3jcm title: Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP [more info...] Chain information for 3jcm #1 --- Chain | Description A | Pre-mRNA-splicing factor 8 B | U4/U6 small nuclear ribonucleoprotein PRP4 C | pre-mRNA D | SNR6 snRNA E | SNR14 snRNA F | SNR7-L snRNA G | Pre-mRNA-splicing factor 6 H | Pre-mRNA-splicing factor SNU114 I | Pre-mRNA-processing factor 31 J R | Small nuclear ribonucleoprotein Sm D3 K | U4/U6 small nuclear ribonucleoprotein PRP3 L | Spliceosomal protein DIB1 M | 13 kDa ribonucleoprotein-associated protein N | Pre-mRNA-splicing helicase BRR2 O S | Small nuclear ribonucleoprotein-associated protein B P T | Small nuclear ribonucleoprotein Sm D1 Q U | Small nuclear ribonucleoprotein Sm D2 V Y | Small nuclear ribonucleoprotein E W Z | Small nuclear ribonucleoprotein F X a | Small nuclear ribonucleoprotein G b | U6 snRNA-associated Sm-like protein LSm8 c | U6 snRNA-associated Sm-like protein LSm2 d | U6 snRNA-associated Sm-like protein LSm3 e | U6 snRNA-associated Sm-like protein LSm6 f | U6 snRNA-associated Sm-like protein LSm5 g | U6 snRNA-associated Sm-like protein LSm7 h | U6 snRNA-associated Sm-like protein LSm4 Non-standard residues in 3jcm #1 --- GTP — guanosine-5'-triphosphate M7M — N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) > select clear Alignment identifier is bp1 [1] Associated 3jcm chain B to 3JCM_B with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment bp1 [1] > ui tool show ""Modeller Comparative"" > has active key-value observers (KVO)! These will stop working now that the window is recreated, and will result in exceptions when the observers are removed. Break in QCocoaWindow::recreateWindowIfNeeded to debug. > has active key-value observers (KVO)! These will stop working now that the window is recreated, and will result in exceptions when the observers are removed. Break in QCocoaWindow::recreateWindowIfNeeded to debug. > modeller comparative ""bp1 [1]:2"" multichain false numModels 5 fast false > hetPreserve false hydrogens false tempPath > /Users/blemire/Desktop/untitled_folder waterPreserve false Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/modeller/tool.py"", line 140, in launch_modeller run(self.session, ""modeller comparative %s multichain %s numModels %d fast %s hetPreserve %s"" File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/modeller/cmd.py"", line 34, in sequence_model comparative.model(session, targets, block=block, multichain=multichain, File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/modeller/comparative.py"", line 215, in model pir_target = Sequence(name=opal_safe_file_name(target_name)) UnboundLocalError: local variable 'target_name' referenced before assignment UnboundLocalError: local variable 'target_name' referenced before assignment File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/modeller/comparative.py"", line 215, in model pir_target = Sequence(name=opal_safe_file_name(target_name)) See log for complete Python traceback. OpenGL version: 4.1 ATI-4.5.14 OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac19,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 3.6 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 64 GB System Firmware Version: 1554.120.15.0.0 SMC Version (system): 2.46f12 Software: System Software Overview: System Version: macOS 11.4 (20F71) Kernel Version: Darwin 20.5.0 Time since boot: 4 days 18:53 Graphics/Displays: Radeon Pro 580X: Chipset Model: Radeon Pro 580X Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c0 ROM Revision: 113-D0008A-042 VBIOS Version: 113-D0008A1X-009 EFI Driver Version: 01.B1.042 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Thunderbolt Display: Display Type: LCD Resolution: 2048 x 1152 UI Looks like: 2048 x 1152 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: C02MC33KF2GC Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: Thunderbolt/DisplayPort Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 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 matplotlib-inline: 0.1.2 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: 1.3.0 }}} " defect closed normal Sequence fixed all ChimeraX