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Opened 5 years ago
Closed 5 years ago
#3866 closed defect (fixed)
Corrupted config file
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
ChimeraX wouldn't start (wouldn't show the picture or anything, completely unresponsive). I tried uninstalling/re-installing the latest version and installing the daily build but that didn't fix the issue. I ended up noticing the attached would flash for just a second if I tried to boot the console, so I deleted the \Local\UCSF directory and it boots fine. I'm not sure what I did, but some corrupt file there must've prevented it from starting.
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> C:/Users/bab378/Desktop/Cornell/Thesis/Sondermann_Lab_colab/Flowcharts/FlowchartMapImages_orientationandcolorsession.cxs
Log from Tue Sep 15 15:14:26 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/bab378/Desktop/Cornell/Thesis/Data
> Files/CryoSparc/Exp0056/29Oct2019/cryosparc_P29_J329_006_volume_map_sharp.mrc"
> "C:/Users/bab378/Desktop/Cornell/Thesis/Data
> Files/CryoSparc/Exp0056/29Oct2019/cryosparc_P29_J336_D4final_006_volume_map_sharp.mrc"
Opened cryosparc_P29_J329_006_volume_map_sharp.mrc, grid size 144,144,144,
pixel 1.24, shown at level 0.728, step 1, values float32
Opened cryosparc_P29_J336_D4final_006_volume_map_sharp.mrc, grid size
144,144,144, pixel 1.24, shown at level 1, step 1, values float32
> set bgColor white
> hide #!1 models
> show #!1 models
> select #1
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui tool show "Fit in Map"
Fit map cryosparc_P29_J329_006_volume_map_sharp.mrc in map
cryosparc_P29_J336_D4final_006_volume_map_sharp.mrc using 29838 points
correlation = 0.9657, correlation about mean = 0.7399, overlap = 4.683e+04
steps = 108, shift = 4.23, angle = 10.6 degrees
Position of cryosparc_P29_J329_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P29_J336_D4final_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.04302155 -0.17727278 -0.98322099 188.22586219
-0.56475475 0.80749588 -0.17030115 83.59278541
0.82413665 0.56260534 -0.06537592 -29.61545612
Axis 0.36858635 -0.90893909 -0.19486874
Axis point 125.76769248 -0.00000000 69.33904693
Rotation angle (degrees) 96.16714396
Shift along axis -0.83214055
> ~select #1
Nothing selected
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> hide #!2 models
> save C:\Users\bab378\Desktop\image3.png supersample 3
> show #!2 models
> hide #!2 models
Cannot determine format for
'C:\Users\bab378\Desktop\Cornell\Thesis\Sondermann'
> save
> C:\Users\bab378\Desktop\Cornell\Thesis\Sondermann_Lab_colab\Flowcharts\29Oct2019\Images\csparcJ329.png
> supersample 3
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> save
> C:\Users\bab378\Desktop\Cornell\Thesis\Sondermann_Lab_colab\Flowcharts\29Oct2019\Images\csparcJ336.png
> supersample 3
> open "C:/Users/bab378/Desktop/Cornell/Thesis/Data
> Files/CryoSparc/Exp0056/29Oct2019/job271/run_class001.mrc"
Opened run_class001.mrc, grid size 144,144,144, pixel 1.24, shown at level
0.0321, step 1, values float32
> hide #!2 models
> save
> C:\Users\bab378\Desktop\Cornell\Thesis\Sondermann_Lab_colab\Flowcharts\29Oct2019\Images\relionjob271.png
> supersample 3
> open "C:/Users/bab378/Desktop/Cornell/Thesis/Data
> Files/CryoSparc/Exp0056/29Oct2019/job302/C1_job_postprocess_masked.mrc"
Opened C1_job_postprocess_masked.mrc, grid size 144,144,144, pixel 1.24, shown
at level 0.0563, step 1, values float32
> hide #!3 models
> volume #4 level 0.05626
> save
> C:\Users\bab378\Desktop\Cornell\Thesis\Sondermann_Lab_colab\Flowcharts\29Oct2019\Images\relionjob302.png
> supersample 3
> open "C:/Users/bab378/Desktop/Cornell/Thesis/Data
> Files/CryoSparc/Exp0056/29Oct2019/job316/D4_job316_postprocess_masked.mrc"
Opened D4_job316_postprocess_masked.mrc, grid size 144,144,144, pixel 1.24,
shown at level 0.0548, step 1, values float32
> hide #!4 models
> save
> C:\Users\bab378\Desktop\Cornell\Thesis\Sondermann_Lab_colab\Flowcharts\29Oct2019\Images\relionjob316.png
> supersample 3
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> close #2
> close #3
> close #4
> close #5
> save
> C:/Users/bab378/Desktop/Cornell/Thesis/Sondermann_Lab_colab/Flowcharts/FlowchartMapImages_orientationandcolorsession.cxs
opened ChimeraX session
> open
> D:/Flowcharts/03Mar2020/Images/FinalMaps/C1/cryosparc_P29_J311_006_volume_map_sharp.mrc
Opened cryosparc_P29_J311_006_volume_map_sharp.mrc, grid size 140,140,140,
pixel 1.24, shown at level 0.611, step 1, values float32
> select #2
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui tool show "Fit in Map"
Fit map cryosparc_P29_J311_006_volume_map_sharp.mrc in map
cryosparc_P29_J329_006_volume_map_sharp.mrc using 27427 points
correlation = 0.9706, correlation about mean = 0.5988, overlap = 2.157e+04
steps = 100, shift = 6.63, angle = 8.96 degrees
Position of cryosparc_P29_J311_006_volume_map_sharp.mrc (#2) relative to
cryosparc_P29_J329_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.70327781 0.37529696 -0.60378185 47.06473551
0.51428537 0.31779324 0.79656639 -52.12006509
0.49082674 -0.87072364 0.03048720 116.10856520
Axis -0.83392215 -0.54748624 0.06951731
Axis point 0.00000000 30.03782134 92.97202820
Rotation angle (degrees) 88.52280149
Shift along axis -2.64175196
> ~select #2
Nothing selected
> hide #!1 models
> save C:\Users\bab378\Desktop\image7.png supersample 3
OpenGL version: 3.3.0 NVIDIA 391.25
OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 80X7
OS: Microsoft Windows 10 Education (Build 18363)
Memory: 16,995,201,024
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
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: 2.1.1
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: 1.0
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
File attachment: ChimeraX_bug.PNG
Attachments (1)
Change History (4)
by , 5 years ago
| Attachment: | ChimeraX_bug.PNG added |
|---|
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Corrupted config file |
Need to add better checking that the config file was read without error and is valid.
comment:3 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
ChimeraX now catches config-file parsing errors and reverts to defaults instead of exiting.
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