Changes between Initial Version and Version 1 of Ticket #6758


Ignore:
Timestamp:
May 2, 2022, 11:31:54 AM (3 years ago)
Author:
Eric Pettersen
Comment:

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  • Ticket #6758

    • Property Component Unassigned → Core
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → Crash in event loop

  • Ticket #6758 – Description

    initial v1  
    1414  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
    1515  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
     16Windows fatal exception: code 0xc0000374
     17
     18Current thread 0x00000da8 (most recent call first):
     19  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
     20  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
     21  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
     22  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
     23  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
     24===== Log before crash start =====
     25UCSF ChimeraX version: 1.3 (2021-12-08) 
     26© 2016-2021 Regents of the University of California. All rights reserved. 
     27How to cite UCSF ChimeraX 
     28
     29> ui tool show XMAS
     30
     31> open "C:/Users/zeman/Documents/MassSpec/__RQT
     32> results/HADDOCK_run2/cluster11_1.pdb"
     33
     34Summary of feedback from opening C:/Users/zeman/Documents/MassSpec/__RQT
     35results/HADDOCK_run2/cluster11_1.pdb 
     36--- 
     37warnings | Ignored bad PDB record found on line 1 
     38REMARK FILENAME="complex_343w.pdb0" 
     39 
     40Ignored bad PDB record found on line 2 
     41REMARK =============================================================== 
     42 
     43Ignored bad PDB record found on line 3 
     44REMARK HADDOCK run for complex 
     45 
     46Ignored bad PDB record found on line 4 
     47REMARK initial structure: complex_343.pdb 
     48 
     49Ignored bad PDB record found on line 5 
     50REMARK =============================================================== 
     51 
     5230 messages similar to the above omitted 
     53 
     54Chain information for cluster11_1.pdb #1 
     55--- 
     56Chain | Description 
     57A | No description available 
     58B | No description available 
     59C | No description available 
     60 
     61 
     62Peptide pair mapping of Xi_alternative evidence file:
     63C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
     64SDA/Results_individual/0.5-1 ratio/RQT_sulfo-
     65SDA_05-1_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5.csv 
     66Unique peptide pairs: 98 out of 118 
     67Unique peptide pairs with pseudobonds: 63 
     68Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
     69sulfo-SDA/sulfo-SDA/Results_individual/0.5-1 ratio/RQT_sulfo-
     70SDA_05-1_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.pb 
     71Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
     72SBP sulfo-SDA/sulfo-SDA/Results_individual/0.5-1 ratio/RQT_sulfo-
     73SDA_05-1_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.tsv 
     74 
     75Peptide pair mapping of Xi_alternative evidence file:
     76C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
     77SDA/Results_individual/1-1 ratio/RQT_sulfo-
     78SDA_1-1_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5.csv 
     79Unique peptide pairs: 181 out of 182 
     80Unique peptide pairs with pseudobonds: 92 
     81Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
     82sulfo-SDA/sulfo-SDA/Results_individual/1-1 ratio/RQT_sulfo-
     83SDA_1-1_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.pb 
     84Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
     85SBP sulfo-SDA/sulfo-SDA/Results_individual/1-1 ratio/RQT_sulfo-
     86SDA_1-1_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.tsv 
     87 
     88Peptide pair mapping of Xi_alternative evidence file:
     89C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP sulfo-SDA/sulfo-
     90SDA/Results_individual/2-1 ratio/RQT_sulfo-
     91SDA_2-1_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5.csv 
     92Unique peptide pairs: 204 out of 208 
     93Unique peptide pairs with pseudobonds: 103 
     94Pseudobonds are stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT SBP
     95sulfo-SDA/sulfo-SDA/Results_individual/2-1 ratio/RQT_sulfo-
     96SDA_2-1_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.pb 
     97Mapping information is stored in C:/Users/zeman/Documents/MassSpec/2022-02_RQT
     98SBP sulfo-SDA/sulfo-SDA/Results_individual/2-1 ratio/RQT_sulfo-
     99SDA_2-1_Results_20PercentFDRLink_CSM_xiFDR2.1.5.5_1.tsv 
     100
     101> ~select #2
     102
     103211 pseudobonds, 2 models selected 
     104
     105> ~select #3
     106
     107111 pseudobonds, 1 model selected 
     108
     109> ~select #4
     110
     111Nothing selected 
     112
     113> ~select #2
     114
     115103 pseudobonds, 2 models selected 
     116
     117> ~select #3
     118
     11980 pseudobonds, 1 model selected 
     120
     121> ~select #4
     122
     123Nothing selected 
     124
     125> color #3 #ffaa00 models transparency 0
     126
     127> color #3 #ff8000 models transparency 0
     128
     129> color #4 #f700ff models transparency 0
     130
     131> color #4 #ff0073 models transparency 0
     132
     133> color #4 #0084ff models transparency 0
     134
     135> color #4 #003cff models transparency 0
     136
     137> color #4 #002fff models transparency 0
     138
     139> color #4 #0066ff models transparency 0
     140
     141
     142===== Log before crash end =====
     143
     144Log:
     145UCSF ChimeraX version: 1.3 (2021-12-08) 
     146© 2016-2021 Regents of the University of California. All rights reserved. 
     147How to cite UCSF ChimeraX 
     148
     149
     150
     151
     152OpenGL version: 3.3.0 NVIDIA 457.49
     153OpenGL renderer: GeForce GTX 1060 3GB/PCIe/SSE2
     154OpenGL vendor: NVIDIA Corporation
     155Manufacturer: HP
     156Model: HP EliteDesk 800 G4 TWR
     157OS: Microsoft Windows 10 Education (Build 19044)
     158Memory: 16,948,436,992
     159MaxProcessMemory: 137,438,953,344
     160CPU: 12 Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz
     161OSLanguage: en-GB
     162Locale: ('en_GB', 'cp1252')
     163PyQt5 5.15.2, Qt 5.15.2
     164Installed Packages:
     165    alabaster: 0.7.12
     166    appdirs: 1.4.4
     167    Babel: 2.9.1
     168    backcall: 0.2.0
     169    blockdiag: 2.0.1
     170    certifi: 2021.10.8
     171    cftime: 1.5.1.1
     172    charset-normalizer: 2.0.9
     173    ChimeraX-AddCharge: 1.2.2
     174    ChimeraX-AddH: 2.1.11
     175    ChimeraX-AlignmentAlgorithms: 2.0
     176    ChimeraX-AlignmentHdrs: 3.2
     177    ChimeraX-AlignmentMatrices: 2.0
     178    ChimeraX-Alignments: 2.2.3
     179    ChimeraX-AlphaFold: 1.0
     180    ChimeraX-AltlocExplorer: 1.0.1
     181    ChimeraX-AmberInfo: 1.0
     182    ChimeraX-Arrays: 1.0
     183    ChimeraX-Atomic: 1.31
     184    ChimeraX-AtomicLibrary: 4.2
     185    ChimeraX-AtomSearch: 2.0
     186    ChimeraX-AtomSearchLibrary: 1.0
     187    ChimeraX-AxesPlanes: 2.0
     188    ChimeraX-BasicActions: 1.1
     189    ChimeraX-BILD: 1.0
     190    ChimeraX-BlastProtein: 2.0
     191    ChimeraX-BondRot: 2.0
     192    ChimeraX-BugReporter: 1.0
     193    ChimeraX-BuildStructure: 2.6.1
     194    ChimeraX-Bumps: 1.0
     195    ChimeraX-BundleBuilder: 1.1
     196    ChimeraX-ButtonPanel: 1.0
     197    ChimeraX-CageBuilder: 1.0
     198    ChimeraX-CellPack: 1.0
     199    ChimeraX-Centroids: 1.2
     200    ChimeraX-ChemGroup: 2.0
     201    ChimeraX-Clashes: 2.2.2
     202    ChimeraX-ColorActions: 1.0
     203    ChimeraX-ColorGlobe: 1.0
     204    ChimeraX-ColorKey: 1.5
     205    ChimeraX-CommandLine: 1.1.5
     206    ChimeraX-ConnectStructure: 2.0
     207    ChimeraX-Contacts: 1.0
     208    ChimeraX-Core: 1.3
     209    ChimeraX-CoreFormats: 1.1
     210    ChimeraX-coulombic: 1.3.2
     211    ChimeraX-Crosslinks: 1.0
     212    ChimeraX-Crystal: 1.0
     213    ChimeraX-CrystalContacts: 1.0
     214    ChimeraX-DataFormats: 1.2.2
     215    ChimeraX-Dicom: 1.0
     216    ChimeraX-DistMonitor: 1.1.5
     217    ChimeraX-DistUI: 1.0
     218    ChimeraX-Dssp: 2.0
     219    ChimeraX-EMDB-SFF: 1.0
     220    ChimeraX-ExperimentalCommands: 1.0
     221    ChimeraX-FileHistory: 1.0
     222    ChimeraX-FunctionKey: 1.0
     223    ChimeraX-Geometry: 1.1
     224    ChimeraX-gltf: 1.0
     225    ChimeraX-Graphics: 1.1
     226    ChimeraX-Hbonds: 2.1.2
     227    ChimeraX-Help: 1.2
     228    ChimeraX-HKCage: 1.3
     229    ChimeraX-IHM: 1.1
     230    ChimeraX-ImageFormats: 1.2
     231    ChimeraX-IMOD: 1.0
     232    ChimeraX-IO: 1.0.1
     233    ChimeraX-ItemsInspection: 1.0
     234    ChimeraX-Label: 1.1
     235    ChimeraX-ListInfo: 1.1.1
     236    ChimeraX-Log: 1.1.4
     237    ChimeraX-LookingGlass: 1.1
     238    ChimeraX-Maestro: 1.8.1
     239    ChimeraX-Map: 1.1
     240    ChimeraX-MapData: 2.0
     241    ChimeraX-MapEraser: 1.0
     242    ChimeraX-MapFilter: 2.0
     243    ChimeraX-MapFit: 2.0
     244    ChimeraX-MapSeries: 2.1
     245    ChimeraX-Markers: 1.0
     246    ChimeraX-Mask: 1.0
     247    ChimeraX-MatchMaker: 2.0.4
     248    ChimeraX-MDcrds: 2.6
     249    ChimeraX-MedicalToolbar: 1.0.1
     250    ChimeraX-Meeting: 1.0
     251    ChimeraX-MLP: 1.1
     252    ChimeraX-mmCIF: 2.4
     253    ChimeraX-MMTF: 2.1
     254    ChimeraX-Modeller: 1.2.6
     255    ChimeraX-ModelPanel: 1.2.1
     256    ChimeraX-ModelSeries: 1.0
     257    ChimeraX-Mol2: 2.0
     258    ChimeraX-Morph: 1.0
     259    ChimeraX-MouseModes: 1.1
     260    ChimeraX-Movie: 1.0
     261    ChimeraX-Neuron: 1.0
     262    ChimeraX-Nucleotides: 2.0.2
     263    ChimeraX-OpenCommand: 1.7
     264    ChimeraX-PDB: 2.6.5
     265    ChimeraX-PDBBio: 1.0
     266    ChimeraX-PDBLibrary: 1.0.2
     267    ChimeraX-PDBMatrices: 1.0
     268    ChimeraX-PickBlobs: 1.0
     269    ChimeraX-Positions: 1.0
     270    ChimeraX-PresetMgr: 1.0.1
     271    ChimeraX-PubChem: 2.1
     272    ChimeraX-ReadPbonds: 1.0.1
     273    ChimeraX-Registration: 1.1
     274    ChimeraX-RemoteControl: 1.0
     275    ChimeraX-ResidueFit: 1.0
     276    ChimeraX-RestServer: 1.1
     277    ChimeraX-RNALayout: 1.0
     278    ChimeraX-RotamerLibMgr: 2.0.1
     279    ChimeraX-RotamerLibsDunbrack: 2.0
     280    ChimeraX-RotamerLibsDynameomics: 2.0
     281    ChimeraX-RotamerLibsRichardson: 2.0
     282    ChimeraX-SaveCommand: 1.5
     283    ChimeraX-SchemeMgr: 1.0
     284    ChimeraX-SDF: 2.0
     285    ChimeraX-Segger: 1.0
     286    ChimeraX-Segment: 1.0
     287    ChimeraX-SelInspector: 1.0
     288    ChimeraX-SeqView: 2.4.6
     289    ChimeraX-Shape: 1.0.1
     290    ChimeraX-Shell: 1.0
     291    ChimeraX-Shortcuts: 1.1
     292    ChimeraX-ShowAttr: 1.0
     293    ChimeraX-ShowSequences: 1.0
     294    ChimeraX-SideView: 1.0
     295    ChimeraX-Smiles: 2.1
     296    ChimeraX-SmoothLines: 1.0
     297    ChimeraX-SpaceNavigator: 1.0
     298    ChimeraX-StdCommands: 1.6.1
     299    ChimeraX-STL: 1.0
     300    ChimeraX-Storm: 1.0
     301    ChimeraX-Struts: 1.0
     302    ChimeraX-Surface: 1.0
     303    ChimeraX-SwapAA: 2.0
     304    ChimeraX-SwapRes: 2.1
     305    ChimeraX-TapeMeasure: 1.0
     306    ChimeraX-Test: 1.0
     307    ChimeraX-Toolbar: 1.1
     308    ChimeraX-ToolshedUtils: 1.2
     309    ChimeraX-Tug: 1.0
     310    ChimeraX-UI: 1.13.7
     311    ChimeraX-uniprot: 2.2
     312    ChimeraX-UnitCell: 1.0
     313    ChimeraX-ViewDockX: 1.0.1
     314    ChimeraX-VIPERdb: 1.0
     315    ChimeraX-Vive: 1.1
     316    ChimeraX-VolumeMenu: 1.0
     317    ChimeraX-VTK: 1.0
     318    ChimeraX-WavefrontOBJ: 1.0
     319    ChimeraX-WebCam: 1.0
     320    ChimeraX-WebServices: 1.0
     321    ChimeraX-XMAS: 1.1.1
     322    ChimeraX-Zone: 1.0
     323    colorama: 0.4.4
     324    comtypes: 1.1.10
     325    cxservices: 1.1
     326    cycler: 0.11.0
     327    Cython: 0.29.24
     328    decorator: 5.1.0
     329    docutils: 0.17.1
     330    et-xmlfile: 1.1.0
     331    filelock: 3.0.12
     332    funcparserlib: 0.3.6
     333    grako: 3.16.5
     334    h5py: 3.6.0
     335    html2text: 2020.1.16
     336    idna: 3.3
     337    ihm: 0.21
     338    imagecodecs: 2021.4.28
     339    imagesize: 1.3.0
     340    ipykernel: 5.5.5
     341    ipython: 7.23.1
     342    ipython-genutils: 0.2.0
     343    jedi: 0.18.0
     344    Jinja2: 3.0.1
     345    jupyter-client: 6.1.12
     346    jupyter-core: 4.9.1
     347    kiwisolver: 1.3.2
     348    lxml: 4.6.3
     349    lz4: 3.1.3
     350    MarkupSafe: 2.0.1
     351    matplotlib: 3.4.3
     352    matplotlib-inline: 0.1.3
     353    msgpack: 1.0.2
     354    netCDF4: 1.5.7
     355    networkx: 2.6.3
     356    numexpr: 2.8.0
     357    numpy: 1.21.2
     358    openpyxl: 3.0.9
     359    openvr: 1.16.801
     360    packaging: 21.3
     361    pandas: 1.4.2
     362    ParmEd: 3.2.0
     363    parso: 0.8.3
     364    pickleshare: 0.7.5
     365    Pillow: 8.3.2
     366    pip: 21.2.4
     367    pkginfo: 1.7.1
     368    prompt-toolkit: 3.0.23
     369    psutil: 5.8.0
     370    pycollada: 0.7.1
     371    pydicom: 2.1.2
     372    Pygments: 2.10.0
     373    PyOpenGL: 3.1.5
     374    PyOpenGL-accelerate: 3.1.5
     375    pyparsing: 3.0.6
     376    PyQt5-commercial: 5.15.2
     377    PyQt5-sip: 12.8.1
     378    PyQtWebEngine-commercial: 5.15.2
     379    python-dateutil: 2.8.2
     380    pytz: 2021.3
     381    pywin32: 228
     382    pyzmq: 22.3.0
     383    qtconsole: 5.1.1
     384    QtPy: 1.11.3
     385    QtRangeSlider: 0.1.5
     386    RandomWords: 0.3.0
     387    requests: 2.26.0
     388    scipy: 1.7.1
     389    seaborn: 0.11.2
     390    setuptools: 57.5.0
     391    sfftk-rw: 0.7.1
     392    six: 1.16.0
     393    snowballstemmer: 2.2.0
     394    sortedcontainers: 2.4.0
     395    Sphinx: 4.2.0
     396    sphinx-autodoc-typehints: 1.12.0
     397    sphinxcontrib-applehelp: 1.0.2
     398    sphinxcontrib-blockdiag: 2.0.0
     399    sphinxcontrib-devhelp: 1.0.2
     400    sphinxcontrib-htmlhelp: 2.0.0
     401    sphinxcontrib-jsmath: 1.0.1
     402    sphinxcontrib-qthelp: 1.0.3
     403    sphinxcontrib-serializinghtml: 1.1.5
     404    suds-jurko: 0.6
     405    tables: 3.6.1
     406    tifffile: 2021.4.8
     407    tinyarray: 1.2.3
     408    tornado: 6.1
     409    traitlets: 5.1.1
     410    urllib3: 1.26.7
     411    wcwidth: 0.2.5
     412    webcolors: 1.11.1
     413    wheel: 0.37.0
     414    wheel-filename: 1.3.0
     415    WMI: 1.5.1
     416
     417}}}