id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5927 Attempt to use either positions or matrix file jribeiro@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.14393 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description When trying to open q models file there is an error ""Unrecognized file sufix"" Please describe steps that led to the crash here. Windows fatal exception: access violation Current thread 0x00001404 (most recent call first): File ""d:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""d:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""d:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""d:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 87 in _run_code File ""d:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 197 in _run_module_as_main ===== Log before crash start ===== Startup Messages --- warning | No presets found in custom preset folder D:/ChimeraX 1.2.5 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 .\\\links\\\pdb\\\JAP81880.1-Alphafold.pdb Chain information for JAP81880.1-Alphafold.pdb #1 --- Chain | Description A | No description available > open .\\\links\\\ent\\\pdb3uv1.ent pdb3uv1.ent title: Crystal structure A major allergen from dust mite [more info...] Chain information for pdb3uv1.ent #2 --- Chain | Description | UniProt A B | der F 7 allergen | A1KXH4_DERFA > mmaker #1/a to #2/a 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 pdb3uv1.ent, chain A (#2) with JAP81880.1-Alphafold.pdb, chain A (#1), sequence alignment score = 261.9 RMSD between 78 pruned atom pairs is 1.300 angstroms; (across all 187 pairs: 4.024) > view matrix camera position: 0.74442,0.45361,0.48997,80.848,0.40585,0.2753,-0.87149,-120.54,-0.53021,0.84761,0.020838,-22.47 model positions: #1,0.80697,-0.13432,0.57511,22.326,0.12256,-0.9145,-0.38557,2.8566,0.57773,0.38163,-0.72152,-33.573,#2,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix\ Expected an objects specifier or a view name or a keyword > view matrix camera position: 0.74442,0.45361,0.48997,80.848,0.40585,0.2753,-0.87149,-120.54,-0.53021,0.84761,0.020838,-22.47 model positions: #1,0.80697,-0.13432,0.57511,22.326,0.12256,-0.9145,-0.38557,2.8566,0.57773,0.38163,-0.72152,-33.573,#2,1,0,0,0,0,1,0,0,0,0,1,0 > color confidence = true Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > open n:\temp\model.txt models #1 Unrecognized file suffix '.txt' > open n:/temp/model.txt models #1 Unrecognized file suffix '.txt' > toolshed show QMainWindowLayout::tabPosition called with out-of-bounds value '0' > ui mousemode right ""rotate selected models"" > preset cartoons/nucleotides ribbons/slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > ui tool show ""Model Panel"" > toolshed show QMainWindowLayout::tabPosition called with out-of-bounds value '0' > ui tool show ""Model Panel"" > ui tool show AlphaFold > ui tool show ""Model Panel"" > open n:\temp\model models #1 'n:\temp\model' has no suffix > open n:/temp/model.model models #1 Unrecognized file suffix '.model' > open n:/temp/model.model models #1 Unrecognized file suffix '.model' > open n:/temp/model #1 'n:/temp/model' has no suffix > open n:/temp/model.txt models #1 Unrecognized file suffix '.txt' > open n:/temp/model.txt models #1 Unrecognized file suffix '.txt' > open n:/temp/model.txt Unrecognized file suffix '.txt' > save matrix ""n:\\\temp\\\matrix"" Cannot determine format for 'matrix' > view matrix camera position: 0.7261,0.5211,0.4486,74.629,0.44048,0.14846,-0.8854,-122.63,-0.52798,0.84049,-0.12174,-43.9 model positions: #1,0.80697,-0.13432,0.57511,22.326,0.12256,-0.9145,-0.38557,2.8566,0.57773,0.38163,-0.72152,-33.573,#2,1,0,0,0,0,1,0,0,0,0,1,0 > save model #1/a Cannot determine format for 'model' > save model #1/a ""n:\\\temp\\\matrix"" Cannot determine format for 'model' > save model #1/a Cannot determine format for 'model' > save model #1/a > #1,0.80697,-0.13432,0.57511,22.326,0.12256,-0.9145,-0.38557,2.8566,0.57773,0.38163,-0.72152,-33.573,#2,1,0,0,0,0,1,0,0,0,0,1,0 Cannot determine format for 'model' > save model.txt #1/a > #1,0.80697,-0.13432,0.57511,22.326,0.12256,-0.9145,-0.38557,2.8566,0.57773,0.38163,-0.72152,-33.573,#2,1,0,0,0,0,1,0,0,0,0,1,0 No known data format for file suffix '.txt' > view matrix > mod#1,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908 Expected a keyword > save filename models > #1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908 Cannot determine format for 'filename' > models > #1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908 Unknown command: models #1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908 > close #2 > show target m > hide #1 models > show #1 models > select #1 3265 atoms, 3306 bonds, 208 residues, 1 model selected > ~select #1 Nothing selected QMainWindowLayout::tabPosition called with out-of-bounds value '0' > ave > model.#1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908 Unknown command: ave model.#1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908 > save > model.#1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908 No known data format for file suffix '.291908' > save > model.#1/A,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908 No known data format for file suffix '.291908' > open n:\temp\model.cmx models Unrecognized file suffix '.cmx' ===== Log before crash end ===== Log: Startup Messages --- warning | No presets found in custom preset folder D:/ChimeraX 1.2.5 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 .\\\links\\\pdb\\\JAP81880.1-Alphafold.pdb Chain information for JAP81880.1-Alphafold.pdb #1 --- Chain | Description A | No description available > open .\\\links\\\ent\\\pdb3uv1.ent pdb3uv1.ent title: Crystal structure A major allergen from dust mite [more info...] Chain information for pdb3uv1.ent #2 --- Chain | Description | UniProt A B | der F 7 allergen | A1KXH4_DERFA > mmaker #1 to #2/a 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 pdb3uv1.ent, chain A (#2) with JAP81880.1-Alphafold.pdb, chain A (#1), sequence alignment score = 261.9 RMSD between 78 pruned atom pairs is 1.300 angstroms; (across all 187 pairs: 4.024) > view > open n:\temp\model.cmx models Unrecognized file suffix '.cmx' OpenGL version: 3.3 (Core Profile) Mesa 20.2.0-devel (git-a8d28e4676) OpenGL renderer: llvmpipe (LLVM 5.0, 256 bits) OpenGL vendor: VMware, Inc. Manufacturer: VMware, Inc. Model: VMware Virtual Platform OS: Microsoft Windows Server 2016 Standard (Build 14393) Memory: 25,769,332,736 MaxProcessMemory: 137,438,953,344 CPU: 1 Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz OSLanguage: en-US Locale: ('en_US', '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: 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-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 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 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 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 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 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 pywin32: 228 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 WMI: 1.5.1 File attachment: model.cmx }}} [attachment:""model.cmx""] " defect closed normal Graphics not a bug Elaine Meng all ChimeraX