id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8383 cannot import name '_log_alphafold_chain_table' hholme@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19044 ChimeraX Version: 1.6.dev202211190159 (2022-11-19 01:59:55 UTC) Description probably from running chimerax on two computers without all the same input data. tried running new alphafold prediction from existing file of a multimer prediction, and got results but it may not have known where to go to continue chain prediction. Probably not a problem you should try to fix.(Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.6.dev202211190159 (2022-11-19) © 2016-2022 Regents of the University of California. All rights reserved. > open ""G:\My Drive\0_DUF1220_202208\0_ALPHAFOLD2_ RESULTS\X117_results\X117 > CASK 182 aa 3 contacts connect two long strings.cxs"" format session Log from Sun Jan 29 11:54:00 2023 > open C:\Users\17202\Downloads\ChimeraX\AlphaFold\chain_images.py Error running startup command 'open ""C:\Users\17202\Downloads\ChimeraX\AlphaFold\chain_images.py""': No such file/path: C:\Users\17202\Downloads\ChimeraX\AlphaFold\chain_images.py UCSF ChimeraX version: 1.6.dev202211190159 (2022-11-19) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX QOpenGLShader::compile(Fragment): ERROR: 4:1: 'textureSampler' : syntax error syntax error *** Problematic Fragment shader source code *** #version 110 #ifdef GL_KHR_blend_equation_advanced #extension GL_ARB_fragment_coord_conventions : enable #extension GL_KHR_blend_equation_advanced : enable #endif #define lowp #define mediump #define highp #line 1 varying highp vec2 uv;uniform sampler2DRect textureSampler;uniform bool swizzle;uniform highp float opacity;void main() { highp vec4 tmpFragColor = texture2DRect(textureSampler,uv); tmpFragColor.a *= opacity; gl_FragColor = swizzle ? tmpFragColor.bgra : tmpFragColor;} *** QOpenGLShader::compile(Fragment): ERROR: 4:1: 'textureSampler' : syntax error syntax error *** Problematic Fragment shader source code *** #version 110 #ifdef GL_KHR_blend_equation_advanced #extension GL_ARB_fragment_coord_conventions : enable #extension GL_KHR_blend_equation_advanced : enable #endif #define lowp #define mediump #define highp #line 1 varying highp vec2 uv;uniform sampler2DRect textureSampler;uniform bool swizzle;uniform highp float opacity;void main() { highp vec4 tmpFragColor = texture2DRect(textureSampler,uv); tmpFragColor.a *= opacity; gl_FragColor = swizzle ? tmpFragColor.bgra : tmpFragColor;} *** > open ""G:/My Drive/0_DUF1220_202208/0_ALPHAFOLD2_ > RESULTS/0_ALPHAFOLD2_CHIMERAX_IMAGES"" format dicom > save ""G:/My Drive/0_DUF1220_202208/0_ALPHAFOLD2_ RESULTS/20230129 X > CON2.cxs"" > cd ""G:/My Drive/0_DUF1220_202208/0_ALPHAFOLD2_ RESULTS"" Current working directory is: G:\My Drive\0_DUF1220_202208\0_ALPHAFOLD2_ RESULTS > open ""G:/My Drive/0_DUF1220_202208/0_ALPHAFOLD2_ > RESULTS/X117_results/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description B | No description available C | No description available > ui tool show Clashes > clashes 115 clashes > interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0 > areaCutoff 0 3 contacting residues > select /B 572 atoms, 583 bonds, 12 pseudobonds, 72 residues, 2 models selected > color (#!1 & sel) red > select /B 572 atoms, 583 bonds, 12 pseudobonds, 72 residues, 2 models selected > style sel ball Changed 572 atom styles > show sel cartoons > undo > show sel surfaces > select /C 1436 atoms, 1485 bonds, 87 pseudobonds, 182 residues, 2 models selected > save C:\Users\17202\Desktop\image27.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\17202\Desktop\movie4.mp4 Movie saved to \C:Users\\...\Desktop\movie4.mp4 > select /C 1436 atoms, 1485 bonds, 87 pseudobonds, 182 residues, 2 models selected > rainbow sel > style sel ball Changed 1436 atom styles > show sel surfaces > save C:\Users\17202\Desktop\image28.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\17202\Desktop\movie5.mp4 Movie saved to \C:Users\\...\Desktop\movie5.mp4 > save ""G:/My Drive/0_DUF1220_202208/0_ALPHAFOLD2_ RESULTS/X117_results/X117 > CASK 182 aa 3 contacts connect two long strings.cxs"" ——— End of log from Sun Jan 29 11:54:00 2023 ——— opened ChimeraX session > open ""G:/My Drive/0_DUF1220_202208/0_ALPHAFOLD2_ > RESULTS/X117_results/best_model.pdb"" Chain information for best_model.pdb #2 --- Chain | Description B | No description available C | No description available > select ~sel 2580 atoms, 2651 bonds, 12 pseudobonds, 326 residues, 3 models selected > select ~sel 1436 atoms, 1485 bonds, 87 pseudobonds, 182 residues, 2 models selected > select 4016 atoms, 4136 bonds, 115 pseudobonds, 508 residues, 3 models selected > interfaces select #1/B & ::polymer_type>0 contacting #1/C & ::polymer_type>0 > areaCutoff 0 3 contacting residues > interfaces select #1/B & ::polymer_type>0 contacting #1/C & ::polymer_type>0 > areaCutoff 0 3 contacting residues > select #2/C 1436 atoms, 1485 bonds, 182 residues, 1 model selected > interfaces select #1/B & ::polymer_type>0 contacting #1/C & ::polymer_type>0 > areaCutoff 0 3 contacting residues > select clear > select 4016 atoms, 4136 bonds, 115 pseudobonds, 508 residues, 3 models selected > select up 4016 atoms, 4136 bonds, 115 pseudobonds, 508 residues, 5 models selected > interfaces select #1/B & ::polymer_type>0 contacting #1/C & ::polymer_type>0 > areaCutoff 0 3 contacting residues > select down 1 model selected > interfaces select #1/B & ::polymer_type>0 contacting #1/C & ::polymer_type>0 > areaCutoff 0 3 contacting residues > select up 308 atoms, 314 bonds, 38 residues, 2 models selected > show (#!1 & sel) target ab > undo > cartoon (#!1 & sel) > show sel cartoons > show sel surfaces > show sel cartoons > hide sel surfaces > hide sel cartoons [Repeated 1 time(s)] > surface style #1.2 mesh > mlp sel Map values for surface ""best_model.pdb_B SES surface"": minimum -23.97, mean -5.743, maximum 22.56 To also show corresponding color key, enter the above mlp command and add key true > undo > mlp sel Map values for surface ""best_model.pdb_B SES surface"": minimum -23.97, mean -5.743, maximum 22.56 To also show corresponding color key, enter the above mlp command and add key true > undo > ui tool show ""Map Statistics"" > measure mapstats QOpenGLShader::compile(Fragment): ERROR: 4:1: 'textureSampler' : syntax error syntax error *** Problematic Fragment shader source code *** #version 110 #ifdef GL_KHR_blend_equation_advanced #extension GL_ARB_fragment_coord_conventions : enable #extension GL_KHR_blend_equation_advanced : enable #endif #define lowp #define mediump #define highp #line 1 varying highp vec2 uv;uniform sampler2DRect textureSampler;uniform bool swizzle;uniform highp float opacity;void main() { highp vec4 tmpFragColor = texture2DRect(textureSampler,uv); tmpFragColor.a *= opacity; gl_FragColor = swizzle ? tmpFragColor.bgra : tmpFragColor;} *** > view orient > select ~sel 3708 atoms, 3818 bonds, 97 pseudobonds, 470 residues, 3 models selected > undo > ui tool show ""Map Coordinates"" > undo > view orient > ui tool show ""Basic Actions"" > undo > ui tool show ""File History"" > undo > ui tool show ""Scale Bar"" > undo > ui tool show ""Altloc Explorer"" > undo > ui tool show ""Cage Builder"" > undo > ui tool show ""Modeller Comparative"" > ui tool show AlphaFold > alphafold match #1/B Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json Fetching compressed AlphaFold A0A075B6G5 from https://alphafold.ebi.ac.uk/files/AF-A0A075B6G5-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A075B6G5 (chain B) AlphaFold chains matching best_model.pdb --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id B | A0A075B6G5_HUMAN | A0A075B6G5 | 99.22 | 72 | 72 | 100 Opened 1 AlphaFold model > alphafold match #1/C Fetching compressed AlphaFold P07498 from https://alphafold.ebi.ac.uk/files/AF-P07498-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: P07498 (chain C) AlphaFold chains matching best_model.pdb --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id C | CASK_HUMAN | P07498 | 119.07 | 182 | 182 | 100 Opened 1 AlphaFold model > alphafold predict #1/C Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. QOpenGLShader::compile(Fragment): ERROR: 4:1: 'textureSampler' : syntax error syntax error *** Problematic Fragment shader source code *** #version 110 #ifdef GL_KHR_blend_equation_advanced #extension GL_ARB_fragment_coord_conventions : enable #extension GL_KHR_blend_equation_advanced : enable #endif #define lowp #define mediump #define highp #line 1 varying highp vec2 uv;uniform sampler2DRect textureSampler;uniform bool swizzle;uniform highp float opacity;void main() { highp vec4 tmpFragColor = texture2DRect(textureSampler,uv); tmpFragColor.a *= opacity; gl_FragColor = swizzle ? tmpFragColor.bgra : tmpFragColor;} *** Running AlphaFold prediction AlphaFold prediction finished Results in C:\Users\17202/Downloads/ChimeraX/AlphaFold/prediction_6 > open C:\Users\17202/Downloads/ChimeraX/AlphaFold/prediction_6\best_model.pdb Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\alphafold\predict.py"", line 233, in _unzip_results self._open_prediction() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\alphafold\predict.py"", line 214, in _open_prediction self.session.models.add(models) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 721, in add m.added_to_session(session) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\alphafold\fetch.py"", line 96, in _show_chain_table from .match import _log_alphafold_chain_table ImportError: cannot import name '_log_alphafold_chain_table' from 'chimerax.alphafold.match' (C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\alphafold\match.py) ImportError: cannot import name '_log_alphafold_chain_table' from 'chimerax.alphafold.match' (C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\alphafold\match.py) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\alphafold\fetch.py"", line 96, in _show_chain_table from .match import _log_alphafold_chain_table See log for complete Python traceback. OpenGL version: 3.3.0 - Build 20.19.15.4531 OpenGL renderer: Intel(R) HD Graphics 4400 OpenGL vendor: Intel Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: LENOVO Model: 20B7S1TB07 OS: Microsoft Windows 10 Pro (Build 19044) Memory: 12,555,984,896 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i7-4600U CPU @ 2.10GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.5.5 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.8 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.43.4 ChimeraX-AtomicLibrary: 8.0.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202211190159 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.9 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.7 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.3 ChimeraX-PDB: 2.6.9 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.25.2 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.6 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.3 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.0.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.0.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 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 stack-data: 0.6.1 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.10.0 }}} " defect closed normal Structure Prediction fixed all ChimeraX