id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4099 No matching residues in matchmaker sequence alignment yoavnavott@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description When displaying pairwise sequence alignment after using matchmaker, the aligned sequences do not have any matched residue regions and when closing the sequence window an error pops up saying ""No statusbar messages will be shown due to inadequate OpenGL"". Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui dockable false ""Volume Viewer"" > ui dockable true ""Volume Viewer"" > toolshed show > ui tool show Updates > ui tool show Updates > interfaces ~solvent No atoms specified > graphics quality Traceback (most recent call last): File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py"", line 275, in execute cmd.run(cmd_text) File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\std_commands\graphics.py"", line 167, in graphics_quality dmin, dmax = min(div), max(div) ValueError: min() arg is an empty sequence ValueError: min() arg is an empty sequence File ""D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\std_commands\graphics.py"", line 167, in graphics_quality dmin, dmax = min(div), max(div) See log for complete Python traceback. > graphics quality 1 > graphics quality Traceback (most recent call last): File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py"", line 275, in execute cmd.run(cmd_text) File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\std_commands\graphics.py"", line 167, in graphics_quality dmin, dmax = min(div), max(div) ValueError: min() arg is an empty sequence ValueError: min() arg is an empty sequence File ""D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\std_commands\graphics.py"", line 167, in graphics_quality dmin, dmax = min(div), max(div) See log for complete Python traceback. > graphics quality 5 > ui tool show Updates > open D:/Downloads/peclyases.cxc > open 1jta Summary of feedback from opening 1jta fetched from pdb --- note | Fetching compressed mmCIF 1jta from http://files.rcsb.org/download/1jta.cif 1jta title: Crystal Structure of Pectate Lyase A (C2 form) [more info...] Chain information for 1jta #1 --- Chain | Description A | pectate lyase A Non-standard residues in 1jta #1 --- SO4 — sulfate ion > open 1bn8 Summary of feedback from opening 1bn8 fetched from pdb --- notes | Fetching compressed mmCIF 1bn8 from http://files.rcsb.org/download/1bn8.cif Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif 1bn8 title: Bacillus subtilis pectate lyase [more info...] Chain information for 1bn8 #2 --- Chain | Description A | protein (pectate lyase) Non-standard residues in 1bn8 #2 --- CA — calcium ion > open 2pec Summary of feedback from opening 2pec fetched from pdb --- note | Fetching compressed mmCIF 2pec from http://files.rcsb.org/download/2pec.cif 2pec title: The refined three-dimensional structure of pectate lyase C from erwinia chrysanthemi At 2.2 angstroms resolution: implications for an enzymatic mechanism [more info...] Chain information for 2pec #3 --- Chain | Description A | pectate lyase C > color #1 gold > color #2 deep sky blue > color #3 hot pink > hide > cartoon style xsection rectangle > mmaker #2 to #1 show t 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 1jta, chain A (#1) with 1bn8, chain A (#2), sequence alignment score = 813.4 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 1jta #1/A, 1bn8 #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 273 pruned atom pairs is 0.843 angstroms; (across all 347 pairs: 2.376) > mmaker #3 to #1 show t 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 1jta, chain A (#1) with 2pec, chain A (#3), sequence alignment score = 341.2 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: 1jta #1/A, 2pec #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 148 pruned atom pairs is 0.961 angstroms; (across all 296 pairs: 8.794) > set silhouettes true > set bgColor white > lighting gentle executed peclyases.cxc Alignment identifier is 1/A Alignment identifier is 2/A Alignment identifier is 3/A > sequence header 1 conservation setting initially_shown False > sequence header 1 conservation setting initially_shown True > sequence header 1 conservation setting initially_shown False > sequence header 1 rmsd setting initially_shown True No statusbar messages will be shown due to inadequate OpenGL > graphics rate true > graphics rate false No statusbar messages will be shown due to inadequate OpenGL No statusbar messages will be shown due to inadequate OpenGL No statusbar messages will be shown due to inadequate OpenGL No statusbar messages will be shown due to inadequate OpenGL > ui tool show Matchmaker OpenGL version: 3.3.0 NVIDIA 460.89 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: System manufacturer Model: System Product Name OS: Microsoft Windows 10 Pro N (Build 19042) Memory: 17,113,600,000 MaxProcessMemory: 137,438,953,344 CPU: 16 AMD Ryzen 7 1700 Eight-Core Processor "" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 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: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 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: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 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 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 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: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 gdcm: 2.8.8 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5+mkl numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pywin32: 228 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 WMI: 1.5.1 }}} " defect closed normal Graphics fixed Tom Goddard all ChimeraX