id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6978 Blocking not honored for web jobs Eric Pettersen Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.4.dev202204260114 (2022-04-26 01:14:38 UTC) Description Web jobs not honoring blocking. The modeller/color command in the included log immediately colors all models red, before any results are returned. Log: UCSF ChimeraX version: 1.4.dev202204260114 (2022-04-26) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/pett/src/chimerax/src/bundles/alignments/test-data/nonassoc.fa > format fasta Summary of feedback from opening /Users/pett/src/chimerax/src/bundles/alignments/test-data/nonassoc.fa --- notes | Alignment identifier is nonassoc.fa Showing conservation header (""seq_conservation"" residue attribute) for alignment nonassoc.fa Opened 5 sequences from nonassoc.fa > open 1qvc 1qvc title: Crystal structure analysis of single stranded DNA binding protein (SSB) from E.coli [more info...] Chain information for 1qvc #1 --- Chain | Description | UniProt A B C D | single stranded DNA binding protein monomer | SSB_ECOLI Associated 1qvc chain A to 1qvc with 0 mismatches Associated 1qvc chain B to 1qvc with 0 mismatches Associated 1qvc chain C to 1qvc with 0 mismatches Associated 1qvc chain D to 1qvc with 0 mismatches > help modeller > modeller comparative :T0151 block true > color red Webservices job id: REHA45RXP8HLBJ5F QMainWindowLayout::tabPosition called with out-of-bounds value '0' Modeller job ID REHA45RXP8HLBJ5F finished Parameters --- Chain pairing | ss 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 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment score = 287.8 Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment score = 319 Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment score = 289.2 Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment score = 284.4 RMSD between 386 pruned atom pairs is 0.511 angstroms; (across all 569 pairs: 8.289) Parameters --- Chain pairing | ss 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 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment score = 298.6 Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment score = 301 Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment score = 289.2 Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment score = 284.4 RMSD between 391 pruned atom pairs is 0.497 angstroms; (across all 569 pairs: 8.234) Parameters --- Chain pairing | ss 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 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment score = 316.6 Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment score = 297.4 Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment score = 283.2 Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment score = 280.8 RMSD between 387 pruned atom pairs is 0.488 angstroms; (across all 569 pairs: 8.228) Parameters --- Chain pairing | ss 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 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment score = 302.2 Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment score = 315.4 Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment score = 288 Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment score = 284.4 RMSD between 388 pruned atom pairs is 0.544 angstroms; (across all 569 pairs: 8.248) Parameters --- Chain pairing | ss 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 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment score = 295 Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment score = 304.6 Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment score = 277.2 Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment score = 284.4 RMSD between 383 pruned atom pairs is 0.574 angstroms; (across all 569 pairs: 8.312) Associated T0151 chain A to T0151 with 0 mismatches Associated T0151 chain B to T0151 with 0 mismatches Associated T0151 chain C to T0151 with 0 mismatches Associated T0151 chain D to T0151 with 0 mismatches Associated T0151 chain A to T0151 with 0 mismatches Associated T0151 chain B to T0151 with 0 mismatches Associated T0151 chain C to T0151 with 0 mismatches Associated T0151 chain D to T0151 with 0 mismatches Associated T0151 chain A to T0151 with 0 mismatches Associated T0151 chain B to T0151 with 0 mismatches Associated T0151 chain C to T0151 with 0 mismatches Associated T0151 chain D to T0151 with 0 mismatches Associated T0151 chain A to T0151 with 0 mismatches Associated T0151 chain B to T0151 with 0 mismatches Associated T0151 chain C to T0151 with 0 mismatches Associated T0151 chain D to T0151 with 0 mismatches Associated T0151 chain A to T0151 with 0 mismatches Associated T0151 chain B to T0151 with 0 mismatches Associated T0151 chain C to T0151 with 0 mismatches Associated T0151 chain D to T0151 with 0 mismatches Chain information for T0151 --- Chain | Description 2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.1/B 2.2/B 2.3/B 2.4/B 2.5/B 2.1/C 2.2/C 2.3/C 2.4/C 2.5/C 2.1/D 2.2/D 2.3/D 2.4/D 2.5/D | No description available OpenGL version: 4.1 INTEL-14.7.23 OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Memory: 16 GB Boot ROM Version: 428.60.3.0.0 SMC Version (system): 2.32f21 Software: System Software Overview: System Version: macOS 10.15.7 (19H1824) Kernel Version: Darwin 19.6.0 Time since boot: 8:06 Graphics/Displays: Intel Iris Pro Graphics 6200: Chipset Model: Intel Iris Pro Graphics 6200 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1622 Revision ID: 0x000a Metal: Supported, feature set macOS GPUFamily1 v4 Displays: iMac: Display Type: LCD Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.38.2 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.3 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202204260114 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: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 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: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 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: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 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: 2.6 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16.5 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 1.1.0 ChimeraX-XMAS: 1.1.1 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 et-xmlfile: 1.1.0 filelock: 3.4.2 fonttools: 4.33.2 funcparserlib: 1.0.0a1 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 MolecularDynamicsViewer: 1.4 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openpyxl: 3.0.9 openvr: 1.16.802 packaging: 21.0 pandas: 1.4.2 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.8 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 22.3.0 qtconsole: 5.3.0 QtPy: 2.0.1 QtRangeSlider: 0.1.5 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 seaborn: 0.11.2 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 File attachment: nonassoc.fa }}} [attachment:""nonassoc.fa""] " defect closed blocker 1.5 Infrastructure fixed 5223 all ChimeraX