id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6184 color byattribute failure r.m.vandenbos@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19042 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Running the command: color byattr seq_conservation PDB open ClustalW alignment.aln Log: Startup Messages --- warning | Your computer has Intel graphics driver 7157 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this. note | available bundle cache has not been initialized yet 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 ""\\\soliscom.uu.nl\users\4114914\My > Documents\Desktop\Proteome_Unpolished\Models_homologues\Natamycinase_modeller.pdb"" > format pdb Chain information for Natamycinase_modeller.pdb #1 --- Chain | Description X | No description available > open ""//soliscom.uu.nl/users/4114914/My > Documents/Desktop/Alignment_Aspergillus.aln"" Summary of feedback from opening //soliscom.uu.nl/users/4114914/My Documents/Desktop/Alignment_Aspergillus.aln --- notes | Alignment identifier is Alignment_Aspergillus.aln Associated Natamycinase_modeller.pdb chain X to Natamycinase with 0 mismatches Showing consensus header (""seq_consensus"" residue attribute) for alignment Alignment_Aspergillus.aln Showing conservation header (""seq_conservation"" residue attribute) for alignment Alignment_Aspergillus.aln Opened 8 sequences from Alignment_Aspergillus.aln > color byattribute seq_conservation Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\std_commands\color.py"", line 1194, in color_by_attr acolors = _value_colors(palette, range, attr_vals) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\std_commands\color.py"", line 1287, in _value_colors cmap = _colormap_with_range(palette, r, default = 'blue-white-red') File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\surface\colorvol.py"", line 164, in _colormap_with_range cm = cmap.linear_range(vmin, vmax) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\colors.py"", line 334, in linear_range v = numpy.linspace(min_value, max_value, len(self.colors)) File ""<__array_function__ internals>"", line 5, in linspace File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\numpy\core\function_base.py"", line 127, in linspace start = asanyarray(start) * 1.0 numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype(' None numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype(' None File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\numpy\core\function_base.py"", line 127, in linspace start = asanyarray(start) * 1.0 See log for complete Python traceback. > color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4 > noValueColor yellow Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\std_commands\color.py"", line 1194, in color_by_attr acolors = _value_colors(palette, range, attr_vals) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\std_commands\color.py"", line 1290, in _value_colors colors = cmap.interpolated_rgba8(values) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\colors.py"", line 322, in interpolated_rgba8 c = self.interpolated_rgba(values) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\colors.py"", line 316, in interpolated_rgba colors = map.interpolate_colormap(values, self.data_values, self.colors, TypeError: Array argument has non-numeric values TypeError: Array argument has non-numeric values File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\colors.py"", line 316, in interpolated_rgba colors = map.interpolate_colormap(values, self.data_values, self.colors, See log for complete Python traceback. > color byattribute seq_conservation Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\std_commands\color.py"", line 1194, in color_by_attr acolors = _value_colors(palette, range, attr_vals) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\std_commands\color.py"", line 1287, in _value_colors cmap = _colormap_with_range(palette, r, default = 'blue-white-red') File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\surface\colorvol.py"", line 164, in _colormap_with_range cm = cmap.linear_range(vmin, vmax) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\colors.py"", line 334, in linear_range v = numpy.linspace(min_value, max_value, len(self.colors)) File ""<__array_function__ internals>"", line 5, in linspace File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\numpy\core\function_base.py"", line 127, in linspace start = asanyarray(start) * 1.0 numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype(' None numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype(' None File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\numpy\core\function_base.py"", line 127, in linspace start = asanyarray(start) * 1.0 See log for complete Python traceback. > select /X:46-47 12 atoms, 11 bonds, 2 residues, 1 model selected > select /X:46-48 21 atoms, 20 bonds, 3 residues, 1 model selected > color byattribute seq_conservation Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\std_commands\color.py"", line 1194, in color_by_attr acolors = _value_colors(palette, range, attr_vals) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\std_commands\color.py"", line 1287, in _value_colors cmap = _colormap_with_range(palette, r, default = 'blue-white-red') File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\surface\colorvol.py"", line 164, in _colormap_with_range cm = cmap.linear_range(vmin, vmax) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\colors.py"", line 334, in linear_range v = numpy.linspace(min_value, max_value, len(self.colors)) File ""<__array_function__ internals>"", line 5, in linspace File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\numpy\core\function_base.py"", line 127, in linspace start = asanyarray(start) * 1.0 numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype(' None numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype(' None File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\numpy\core\function_base.py"", line 127, in linspace start = asanyarray(start) * 1.0 See log for complete Python traceback. QMainWindowLayout::tabPosition called with out-of-bounds value '0' > color byattribute seq_conservation Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\std_commands\color.py"", line 1194, in color_by_attr acolors = _value_colors(palette, range, attr_vals) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\std_commands\color.py"", line 1287, in _value_colors cmap = _colormap_with_range(palette, r, default = 'blue-white-red') File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\surface\colorvol.py"", line 164, in _colormap_with_range cm = cmap.linear_range(vmin, vmax) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\colors.py"", line 334, in linear_range v = numpy.linspace(min_value, max_value, len(self.colors)) File ""<__array_function__ internals>"", line 5, in linspace File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\numpy\core\function_base.py"", line 127, in linspace start = asanyarray(start) * 1.0 numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype(' None numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype(' None File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\numpy\core\function_base.py"", line 127, in linspace start = asanyarray(start) * 1.0 See log for complete Python traceback. OpenGL version: 3.3.0 - Build 26.20.100.7157 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Manufacturer: HP Model: HP EliteDesk 800 G5 TWR OS: Microsoft Windows 10 Enterprise (Build 19042) Memory: 16,943,194,112 MaxProcessMemory: 137,438,953,344 CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz OSLanguage: en-US Locale: ('nl_NL', '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 }}} " defect closed normal Structure Analysis fixed Tom Goddard all ChimeraX