Opened 3 years ago

Closed 3 years ago

#8440 closed defect (can't reproduce)

Clipper: crash setting aniso_u6

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Tom Goddard, Zach Pearson
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.2-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 0x0000000100fa4580 (most recent call first):
  File "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/7B8236A3-F109-43E5-9C57-736689D08CB4/d/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/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/sanity_check.py", line 12 in remove_invalid_anisou
  File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 667 in _anisou_sanity_check
  File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 636 in add_model
  File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 594 in __init__
  File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 170 in _get_symmetry_handler
  File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 159 in get_symmetry_handler
  File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 814 in _change_selected_model
  File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 771 in change_selected_model
  File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 433 in selected_model
  File "/Users/zekecook/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/ui/main_win.py", line 157 in _set_selected_model
  File "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/7B8236A3-F109-43E5-9C57-736689D08CB4/d/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 "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/7B8236A3-F109-43E5-9C57-736689D08CB4/d/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 "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/7B8236A3-F109-43E5-9C57-736689D08CB4/d/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 "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/7B8236A3-F109-43E5-9C57-736689D08CB4/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/57/lgvwg0s92qz_0_6q78v2dqp00000gn/T/AppTranslocation/7B8236A3-F109-43E5-9C57-736689D08CB4/d/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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      "rolloutId" : "5f72dc58705eff005a46b3a9",
      "factorPackIds" : {

      },
      "deploymentId" : 240000015
    }
  ],
  "experiments" : [

  ]
}
}
===== 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  

> open /Users/zekecook/Downloads/cryosparc_P34_J148_006_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P34_J148_006_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 1.05, shown at level 0.0959, step 2, values float32  

> ui tool show Toolbar

> surface dust #1 size 10.5

> volume #1 step 1

> volume #1 level 0.2263

> open /Users/zekecook/Desktop/PI3k_Rab1a_Retry.pdb format pdb

Summary of feedback from opening /Users/zekecook/Desktop/PI3k_Rab1a_Retry.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 23
ASP A 34 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLN A 70 ARG A 74 1
5  
Start residue of secondary structure not found: HELIX 3 3 ILE A 76 ARG A 82 1
7  
Start residue of secondary structure not found: HELIX 4 4 ASP A 95 ASN A 100 1
6  
Start residue of secondary structure not found: HELIX 5 5 ASN A 101 ALA A 113
1 13  
18 messages similar to the above omitted  
  
Chain information for PI3k_Rab1a_Retry.pdb  
---  
Chain | Description  
2.1/A | No description available  
2.2/A | No description available  
2.1/B | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.  

> hide #!2.1 models

> fitmap #2.2 inMap #1

Fit molecule PI3k_Rab1a_Retry.pdb (#2.2) to map
cryosparc_P34_J148_006_volume_map_sharp.mrc (#1) using 30838 atoms  
average map value = 0.1779, steps = 312  
shifted from previous position = 39.3  
rotated from previous position = 11.6 degrees  
atoms outside contour = 20576, contour level = 0.22631  
  
Position of PI3k_Rab1a_Retry.pdb (#2.2) relative to
cryosparc_P34_J148_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98567266 -0.16809755 0.01387902 41.84078500  
0.16859658 0.97948512 -0.11038155 -29.39171457  
0.00496058 0.11114003 0.99379238 8.54032225  
Axis 0.54950326 0.02212295 0.83519862  
Axis point 194.74274874 135.95929844 0.00000000  
Rotation angle (degrees) 11.62850865  
Shift along axis 29.47428163  
  

> select add #2.2

30838 atoms, 31171 bonds, 11 pseudobonds, 1987 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2.2,0.32553,0.79554,0.51103,-152.4,0.88319,-0.062843,-0.46478,143.28,-0.33763,0.60264,-0.72307,311.73

> view matrix models
> #2.2,0.7302,0.5662,0.3824,-154.42,0.68001,-0.54795,-0.48717,303.59,-0.066304,0.61577,-0.78513,266.08

> ui mousemode right "translate selected models"

> view matrix models
> #2.2,0.7302,0.5662,0.3824,-154.5,0.68001,-0.54795,-0.48717,301.48,-0.066304,0.61577,-0.78513,266.88

> view matrix models
> #2.2,0.7302,0.5662,0.3824,-141.24,0.68001,-0.54795,-0.48717,286.76,-0.066304,0.61577,-0.78513,247.9

> fitmap #2.2 inMap #1

Fit molecule PI3k_Rab1a_Retry.pdb (#2.2) to map
cryosparc_P34_J148_006_volume_map_sharp.mrc (#1) using 30838 atoms  
average map value = 0.325, steps = 300  
shifted from previous position = 19.8  
rotated from previous position = 39 degrees  
atoms outside contour = 12287, contour level = 0.22631  
  
Position of PI3k_Rab1a_Retry.pdb (#2.2) relative to
cryosparc_P34_J148_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98306406 -0.00791656 0.18309117 -19.89784471  
0.13535515 -0.64216347 -0.75452307 460.82827021  
0.12354768 0.76652685 -0.63021628 130.42968649  
Axis 0.99483790 0.03894423 0.09370641  
Axis point 0.00000000 200.56018034 173.71460686  
Rotation angle (degrees) 130.14002635  
Shift along axis 10.37356890  
  

> show #!2.1 models

> delete #2.1/B

> select subtract #2.2

Nothing selected  

> select add #2.1

1460 atoms, 1426 bonds, 6 pseudobonds, 231 residues, 2 models selected  

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models #2.1,1,0,0,-18.43,0,1,0,64.662,0,0,1,-21.091

> ui mousemode right "rotate selected models"

> view matrix models
> #2.1,0.52681,0.60405,0.59799,-137.15,-0.0063889,0.70633,-0.70786,253.19,-0.84996,0.36908,0.37596,216.65

> view matrix models
> #2.1,0.96442,-0.012619,0.26406,-57.958,0.25334,0.32955,-0.90951,302.81,-0.075546,0.94405,0.32102,-49.706

> view matrix models
> #2.1,0.79127,-0.29242,0.53701,-19.735,0.14293,-0.76544,-0.62743,474.95,0.59452,0.57322,-0.56388,36.713

> ui mousemode right "translate selected models"

> view matrix models
> #2.1,0.79127,-0.29242,0.53701,9.1647,0.14293,-0.76544,-0.62743,466.45,0.59452,0.57322,-0.56388,37.095

> view matrix models
> #2.1,0.79127,-0.29242,0.53701,8.861,0.14293,-0.76544,-0.62743,452.75,0.59452,0.57322,-0.56388,48.193

> hide #!2.2 models

> fitmap #2.1 inMap #1

Fit molecule PI3k_Rab1a_Retry.pdb (#2.1) to map
cryosparc_P34_J148_006_volume_map_sharp.mrc (#1) using 1460 atoms  
average map value = 0.31, steps = 108  
shifted from previous position = 3.43  
rotated from previous position = 22.5 degrees  
atoms outside contour = 536, contour level = 0.22631  
  
Position of PI3k_Rab1a_Retry.pdb (#2.1) relative to
cryosparc_P34_J148_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.95528845 -0.16770309 0.24351521 3.73629317  
-0.00462622 -0.83196625 -0.55480696 483.58552954  
0.29563928 0.52887412 -0.79554358 168.74859664  
Axis 0.98774935 -0.04750984 0.14864066  
Axis point 0.00000000 216.49245741 157.26935693  
Rotation angle (degrees) 146.73166848  
Shift along axis 5.79835349  
  

> color #1 #3ebfb8ff models

> color #1 #3ebfb87e models

> show #!2.2 models

> open
> /Users/zekecook/Downloads/PI3KC3C2_f0bf3/PI3KC3C2_f0bf3_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
PI3KC3C2_f0bf3_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> ui tool show Matchmaker

> matchmaker #3 to #1

No 'to' model specified  

> matchmaker #3 to #2.2

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 PI3k_Rab1a_Retry.pdb, chain B (#2.2) with
PI3KC3C2_f0bf3_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#3), sequence alignment score = 5258.1  
RMSD between 823 pruned atom pairs is 1.043 angstroms; (across all 1156 pairs:
2.112)  
  

> hide #!2.1 models

> show #!2.1 models

> hide #!2.2 models

> isolde start

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

Populating font family aliases took 74 ms. Replace uses of missing font family
"Carlito" with one that exists to avoid this cost.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 483 residues in model #3 to IUPAC-IUB
standards.  


===== 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 Pro
      Model Identifier: MacBookPro17,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 7429.81.3
      OS Loader Version: 7429.81.3

Software:

    System Software Overview:

      System Version: macOS 12.2 (21D49)
      Kernel Version: Darwin 21.3.0
      Time since boot: 1 day 19:22

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
        U32J59x:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 3840 x 2160 @ 30.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes


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 (3)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Clipper: crash setting aniso_u6

Maybe it's setting aniso_u6 on dead atoms?

in reply to:  2 ; comment:2 by Tristan Croll, 3 years ago 

Running straight from the .dmg again. Lord only knows why *that’s* where it
crashes.

On Mon, 6 Feb 2023 at 17:29, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:3 by Eric Pettersen, 3 years ago

Cc: Tom Goddard Zach Pearson added
Resolution: → can't reproduce
Status: assigned → closed

Right. We hope to make it more obvious that you need to drag the app out of the .dmg by the next release.

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