![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8636 closed defect (duplicate)
Crash clearing aniso_u6
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Tristan Croll | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.2.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000104398580 (most recent call first):
File "/Applications/CryoEM/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 846 in _set_aniso_u6
File "/Users/robinchen/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/sanity_check.py", line 12 in remove_invalid_anisou
File "/Users/robinchen/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 667 in _anisou_sanity_check
File "/Users/robinchen/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 636 in add_model
File "/Users/robinchen/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 594 in __init__
File "/Users/robinchen/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 170 in _get_symmetry_handler
File "/Users/robinchen/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 159 in get_symmetry_handler
File "/Users/robinchen/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 183 in get_map_mgr
File "/Users/robinchen/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/cmd.py", line 122 in associate_volumes
File "/Applications/CryoEM/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/CryoEM/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/CryoEM/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/CryoEM/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/CryoEM/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/CryoEM/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/CryoEM/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/CryoEM/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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"incident" : "90BBBD3C-D2F1-4234-B155-7C574BA2F548",
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"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
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===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold predict
> SNVPAFLTKLWTLVSDPDTDALICWSPSGNSFHVFDQGQFAKEVLPKYFKHNNMASFVRQLNMYGFRKVVHIEQGGLVKPERDDTEFQHPCFLRGQEQLLENIKRKV
> directory /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/DBD_[N]
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/DBD_1
> open
> /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/DBD_1/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
> alphafold predict
> TSVSTLKSEDIKIRQDSVTKLLTDVQLMKGKQECMDSKLLAMKHENEALWREVASLRQKHAQQQKVVNKLIQFLISLVQSNRILGVKRKIPLMLNDSGSAHSMPKYSRQFSLEHVHGSGPYSAPSPAYSSSSLYAPDAVASSGPIISDITELAPASPMASPGGSIDERPLSSSPLVRVKEEPPSPPQSPRVEEASPGRPSSVDTLLSPTALIDSILRESEPAPASVTALTDARGHTDTEGRPPSPPPTSTPEKCLSVAC,TSVSTLKSEDIKIRQDSVTKLLTDVQLMKGKQECMDSKLLAMKHENEALWREVASLRQKHAQQQKVVNKLIQFLISLVQSNRILGVKRKIPLMLNDSGSAHSMPKYSRQFSLEHVHGSGPYSAPSPAYSSSSLYAPDAVASSGPIISDITELAPASPMASPGGSIDERPLSSSPLVRVKEEPPSPPQSPRVEEASPGRPSSVDTLLSPTALIDSILRESEPAPASVTALTDARGHTDTEGRPPSPPPTSTPEKCLSVAC,TSVSTLKSEDIKIRQDSVTKLLTDVQLMKGKQECMDSKLLAMKHENEALWREVASLRQKHAQQQKVVNKLIQFLISLVQSNRILGVKRKIPLMLNDSGSAHSMPKYSRQFSLEHVHGSGPYSAPSPAYSSSSLYAPDAVASSGPIISDITELAPASPMASPGGSIDERPLSSSPLVRVKEEPPSPPQSPRVEEASPGRPSSVDTLLSPTALIDSILRESEPAPASVTALTDARGHTDTEGRPPSPPPTSTPEKCLSVAC
> directory /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/RD_[N]
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/RD_1
> open /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/RD_1/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
B C D | No description available
> open /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/RD_1/best_model.pdb
Chain information for best_model.pdb #3
---
Chain | Description
B C D | No description available
Drag select of 33 residues
> hide #1 models
> open
> /Users/robinchen/Documents/CryoEM/Hongtao/Phenix/DockPredictedModel_2/best_model_processed_docked.pdb
Chain information for best_model_processed_docked.pdb #4
---
Chain | Description
A | No description available
> hide #2 models
> show #2 models
> hide #3 models
> hide #2 models
> open
> /Users/robinchen/Documents/CryoEM/Hongtao/cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc
Opened cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc as #5, grid
size 280,280,280, pixel 1.36, shown at level 0.603, step 2, values float32
> volume #5 level 1.627
> volume #5 step 1
> volume #5 level 1.135
> alphafold predict
> TSVSTLKSEDIKIRQDSVTKLLTDVQLMKGKQECMDSKLLAMKHENEALWREVASLRQKHAQQQKVVNKLIQFLISLVQSNRILGVKRKIPLMLNDSGSAHSMPKYSRQFSLEHVHGSGPYSAPSPAYSSSSLYAPDAVASSGPIISDITELAPASPMASPGGSIDERPLSSSPLVRVKEEPPSPPQSPRVEEASPGRPSSVDTLLSPTALIDSILRESEPAPASVTALTDARGHTDTEGRPPSPPPTSTPEKCLSVAC
> directory /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/RD_[N]
Running AlphaFold prediction
> volume #5 color #b2b2b29e
> show #4 atoms
> open
> /Users/robinchen/Documents/CryoEM/Hongtao/Phenix/DockPredictedModel_2/reduce_failure.pdb
Chain information for reduce_failure.pdb #6
---
Chain | Description
U | No description available
> close #6
> open
> /Users/robinchen/Documents/CryoEM/Hongtao/Phenix/DockPredictedModel_2/best_model_processed_docked_1.pdb
Chain information for best_model_processed_docked_1.pdb #6
---
Chain | Description
A | No description available
> show #1 models
> hide #1 models
> close #1
> close #2
> close #3
> select add #6
876 atoms, 900 bonds, 107 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
876 atoms, 900 bonds, 107 residues, 1 model selected
> select subtract #6
Nothing selected
> hide #6 models
> show #6 models
> log metadata #6
The model has no metadata
> log chains #6
Chain information for best_model_processed_docked_1.pdb #6
---
Chain | Description
A | No description available
> show #6 target m
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
AlphaFold prediction finished
Results in /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/RD_2
> open /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/RD_2/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> ui tool show "Model Loops"
> ui tool show "Fit in Map"
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #1 models
> show #1 models
> hide #4 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> close #1
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> ui favorite true "Model Panel"
> ui favorite false "Model Panel"
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> fitmap #4 inMap #5
Fit molecule best_model_processed_docked.pdb (#4) to map
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) using 876 atoms
average map value = 2.358, steps = 40
shifted from previous position = 0.0546
rotated from previous position = 0.0773 degrees
atoms outside contour = 239, contour level = 1.1347
Position of best_model_processed_docked.pdb (#4) relative to
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999921 -0.00085121 -0.00092993 0.33592622
0.00085165 0.99999952 0.00048055 -0.24183243
0.00092952 -0.00048134 0.99999945 -0.01915081
Axis -0.35644070 -0.68903722 0.63101326
Axis point 44.45449156 0.00000000 374.54430431
Rotation angle (degrees) 0.07730947
Shift along axis 0.03480935
> fitmap #4 inMap #5
Fit molecule best_model_processed_docked.pdb (#4) to map
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) using 876 atoms
average map value = 2.358, steps = 44
shifted from previous position = 0.00253
rotated from previous position = 0.0223 degrees
atoms outside contour = 239, contour level = 1.1347
Position of best_model_processed_docked.pdb (#4) relative to
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999919 -0.00108266 -0.00067013 0.33940731
0.00108310 0.99999920 0.00065638 -0.30255321
0.00066942 -0.00065711 0.99999956 0.04822477
Axis -0.45840439 -0.46750365 0.75584770
Axis point 269.94934072 322.73757604 0.00000000
Rotation angle (degrees) 0.08208599
Shift along axis 0.02230951
> fitmap #4 inMap #5
Fit molecule best_model_processed_docked.pdb (#4) to map
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) using 876 atoms
average map value = 2.357, steps = 40
shifted from previous position = 0.0245
rotated from previous position = 0.0575 degrees
atoms outside contour = 235, contour level = 1.1347
Position of best_model_processed_docked.pdb (#4) relative to
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999910 -0.00046879 -0.00125560 0.32253355
0.00046894 0.99999988 0.00011934 -0.11826045
0.00125554 -0.00011993 0.99999920 -0.15207413
Axis -0.08890896 -0.93310335 0.34844417
Axis point 129.24681377 0.00000000 258.81527663
Rotation angle (degrees) 0.07709632
Shift along axis 0.02868375
> fitmap #4 inMap #5
Fit molecule best_model_processed_docked.pdb (#4) to map
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) using 876 atoms
average map value = 2.358, steps = 40
shifted from previous position = 0.0208
rotated from previous position = 0.0539 degrees
atoms outside contour = 239, contour level = 1.1347
Position of best_model_processed_docked.pdb (#4) relative to
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999911 -0.00105719 -0.00081323 0.35991861
0.00105776 0.99999919 0.00070493 -0.30707617
0.00081249 -0.00070579 0.99999942 0.03620033
Axis -0.46749398 -0.53873974 0.70086295
Axis point 279.09272893 350.18496666 0.00000000
Rotation angle (degrees) 0.08644872
Shift along axis 0.02254583
> fitmap #4 inMap #5
Fit molecule best_model_processed_docked.pdb (#4) to map
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) using 876 atoms
average map value = 2.357, steps = 44
shifted from previous position = 0.0201
rotated from previous position = 0.0413 degrees
atoms outside contour = 234, contour level = 1.1347
Position of best_model_processed_docked.pdb (#4) relative to
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999900 -0.00063223 -0.00126233 0.35621773
0.00063266 0.99999974 0.00033560 -0.18281284
0.00126212 -0.00033639 0.99999915 -0.11349392
Axis -0.23152343 -0.86975699 0.43579775
Axis point 99.46429871 0.00000000 287.07684193
Rotation angle (degrees) 0.08314983
Shift along axis 0.02706959
> fitmap #4 inMap #5
Fit molecule best_model_processed_docked.pdb (#4) to map
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) using 876 atoms
average map value = 2.357, steps = 40
shifted from previous position = 0.00627
rotated from previous position = 0.00528 degrees
atoms outside contour = 234, contour level = 1.1347
Position of best_model_processed_docked.pdb (#4) relative to
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999891 -0.00064316 -0.00132813 0.36789724
0.00064369 0.99999971 0.00039910 -0.19525174
0.00132788 -0.00039995 0.99999904 -0.10221511
Axis -0.26133446 -0.86866185 0.42086922
Axis point 86.83051921 0.00000000 282.92238953
Rotation angle (degrees) 0.08759351
Shift along axis 0.03044431
> fitmap #4 inMap #5
Fit molecule best_model_processed_docked.pdb (#4) to map
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) using 876 atoms
average map value = 2.358, steps = 40
shifted from previous position = 0.0204
rotated from previous position = 0.0216 degrees
atoms outside contour = 238, contour level = 1.1347
Position of best_model_processed_docked.pdb (#4) relative to
cryosparc_P11_cryosparc_P11_J486_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999922 -0.00077494 -0.00097520 0.32618080
0.00077535 0.99999961 0.00042073 -0.22198018
0.00097488 -0.00042149 0.99999944 -0.03702213
Axis -0.32026593 -0.74154819 0.58952186
Axis point 61.34896782 0.00000000 347.00974475
Rotation angle (degrees) 0.07533667
Shift along axis 0.03831905
> hide #4 models
> alphafold predict
> TSVSTLKSEDIKIRQDSVTKLLTDVQLMKGKQECMDSKLLAMKHENEALWREVASLRQKHAQQQKVVNKLIQFLISLVQSNRILGVKRKIPLMLNDSGSAHSMPKYSRQFSLEHVHGSGPYSAPSPAYSSSSLYAPDAVASSGPIISDITELAPASPMASPGGSIDERPLSSSPLVRVKEEPPSPPQSPRVEEASPGRPSSVDTLLSPTALIDSILRESEPAPASVTALTDARGHTDTEGRPPSPPPTSTPEKCLSVAC
> directory /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/RD_[N]
> templates true
Running AlphaFold prediction
> view #6 clip false
> show #6 target m
> log metadata #6
The model has no metadata
> log chains #6
Chain information for best_model_processed_docked_1.pdb #6
---
Chain | Description
A | No description available
> log metadata #6
The model has no metadata
> log chains #6
Chain information for best_model_processed_docked_1.pdb #6
---
Chain | Description
A | No description available
> log metadata #6
The model has no metadata
> log chains #6
Chain information for best_model_processed_docked_1.pdb #6
---
Chain | Description
A | No description available
> select add #6
876 atoms, 900 bonds, 107 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
876 atoms, 900 bonds, 107 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
876 atoms, 900 bonds, 107 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
876 atoms, 900 bonds, 107 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
876 atoms, 900 bonds, 107 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
876 atoms, 900 bonds, 107 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
876 atoms, 900 bonds, 107 residues, 1 model selected
> select subtract #6
Nothing selected
AlphaFold prediction finished
Results in /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/RD_3
> open /Users/robinchen/Documents/CryoEM/Hongtao/AlphaFold/RD_3/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
> close #6
> open
> /Users/robinchen/Documents/CryoEM/Hongtao/Phenix/DockPredictedModel_2/best_model_processed_docked_1.pdb
Chain information for best_model_processed_docked_1.pdb #2
---
Chain | Description
A | No description available
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> close #1
> show #4 models
> hide #4 models
> show #4 models
> hide #2 models
> show #2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> clipper associate #4 toModel #5
Invalid "toModel" argument: must specify 1 structure, got 0 for "#5"
> clipper associate #5 toModel #4
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 7429.81.3
OS Loader Version: 7429.81.3
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 3 days 1:40
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
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-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
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
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 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-ISOLDE: 1.5
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: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
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: 1.9.1
ChimeraX-PDB: 2.6.8
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-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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
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
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
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: 5.1.0
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: 5.1.0
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
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
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
setuptools-scm: 7.0.5
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: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Editing |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash clearing aniso_u6 |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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