id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17215	Crash running modal dialog	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-15.3-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=5.1G written=2843K(0%) resident=2843K(0%) swapped_out=0K(0%) unallocated=5.1G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                           928K       40 \nColorSync                          640K       32 \nCoreAnimation                     1872K       98 \nCoreGraphics                        64K        4 \nCoreServices                       624K        2 \nCoreUI image data                 5344K       42 \nFoundation                          16K        1 \nKernel Alloc Once                   32K        1 \nMALLOC                             4.2G      112 \nMALLOC guard page                  288K       18 \nMach message                        64K        4 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       56.8M       52 \nStack                            370.2M       52 \nVM_ALLOCATE                      358.6M      188 \nVM_ALLOCATE (reserved)            96.0M        2         reserved VM address space (unallocated)\n__AUTH                            5217K      666 \n__AUTH_CONST                      70.3M      913 \n__CTF                               824        1 \n__DATA                            33.0M     1056 \n__DATA_CONST                      34.0M     1074 \n__DATA_DIRTY                      2761K      339 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       637.0M      155 \n__OBJC_RW                         2374K        1 \n__TEXT                             1.2G     1094 \n__TPRO_CONST                       272K        2 \ndyld private memory                 32K        2 \nmapped file                      588.8M      105 \nowned unmapped memory            123.4M        1 \npage table in kernel              2843K        1 \nshared memory                     6800K       34 \n===========                     =======  ======= \nTOTAL                              7.8G     6101 \nTOTAL, minus reserved VM space     7.7G     6101 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""logWritingSignature"" : ""fa9e1c42329a4ae62cd48c46798f9e05e3c44880"",
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""644114de41e7236e6177f9bd"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000013
    },
    {
      ""rolloutId"" : ""639124e81d92412bfb4880b3"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000012
    }
  ],
  ""experiments"" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/Li/Downloads/cryosparc_P19_J324_006_volume_map.mrc

Opened cryosparc_P19_J324_006_volume_map.mrc as #1, grid size 320,320,320,
pixel 0.86, shown at level 0.0182, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.05487

> open /Users/Li/Downloads/cryosparc_P19_J325_005_volume_map.mrc

Opened cryosparc_P19_J325_005_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.86, shown at level 0.0315, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.1041

> open
> /Volumes/data-4T/Projects/校外合作/SunLitao/4-BrxC/cryosparc_P22_J197_006_volume_map_2.8A.mrc

Opened cryosparc_P22_J197_006_volume_map_2.8A.mrc as #3, grid size
360,360,360, pixel 0.86, shown at level 0.0195, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.1218

> select add #2

2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #2,1,0,0,0.77495,0,1,0,8.0807,0,0,1,10.048

> view matrix models #2,1,0,0,1.6505,0,1,0,5.0178,0,0,1,15.851

> view matrix models #2,1,0,0,1.7193,0,1,0,21.674,0,0,1,23.996

> view matrix models #2,1,0,0,2.2683,0,1,0,17.215,0,0,1,26.48

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.74456,-0.51036,0.43032,257.57,0.66035,-0.65757,0.36268,105.67,0.097867,0.5542,0.82661,-40.403

> view matrix models
> #2,-0.97186,-0.23079,-0.04711,316.64,0.17471,-0.84042,0.513,178.19,-0.15799,0.49034,0.85709,0.035788

> view matrix models
> #2,-0.51322,0.51667,0.68532,46.63,-0.22689,-0.85176,0.47225,241.57,0.82773,0.08688,0.55436,-39.481

> view matrix models
> #2,-0.91241,-0.40826,0.028884,322.52,0.40504,-0.89059,0.20687,195.48,-0.05873,0.20045,0.97794,9.8036

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.91241,-0.40826,0.028884,321.38,0.40504,-0.89059,0.20687,210.94,-0.05873,0.20045,0.97794,7.4251

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.92223,0.20238,0.32944,195.89,-0.1075,-0.95268,0.28434,280.49,0.37139,0.22681,0.90035,-45.607

> view matrix models
> #2,-0.77224,-0.62115,0.13346,316.95,0.63507,-0.74867,0.19021,161.31,-0.018231,0.23165,0.97263,-1.8494

> view matrix models
> #2,-0.87087,-0.47625,-0.12155,345.93,0.45779,-0.87595,0.15213,209.13,-0.17892,0.076836,0.98086,41.057

> view matrix models
> #2,-0.86539,-0.48792,-0.11414,345.76,0.48627,-0.87271,0.043792,219.73,-0.12098,-0.017604,0.9925,44.508

> select subtract #2

Nothing selected  

> fitmap #2 inMap #3

Fit map cryosparc_P19_J325_005_volume_map.mrc in map
cryosparc_P22_J197_006_volume_map_2.8A.mrc using 113838 points  
correlation = 0.8731, correlation about mean = 0.533, overlap = 3074  
steps = 148, shift = 15, angle = 19.4 degrees  
  
Position of cryosparc_P19_J325_005_volume_map.mrc (#2) relative to
cryosparc_P22_J197_006_volume_map_2.8A.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.72660305 -0.67512205 0.12750774 331.75652426  
0.68202304 -0.73117434 0.01512144 169.95003582  
0.08302157 0.09795050 0.99172230 -1.92606106  
Axis 0.06088591 0.03270085 0.99760892  
Axis point 132.65843654 149.98299331 0.00000000  
Rotation angle (degrees) 137.14080805  
Shift along axis 23.83535223  
  

> volume #2 level 0.09101

> volume #2 level 0.01624

> ui mousemode right zoom

> volume #2 level 0.08052

> open ""/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex
> 结构预测/AlphaFold3/fold_2025_02_06_16_38_model_0.cif""

Chain information for fold_2025_02_06_16_38_model_0.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Computing secondary structure  

> hide #!3 models

> hide #!2 models

> show #!2 models

> ui mousemode right ""translate selected models""

> select add #4

13472 atoms, 13772 bonds, 1651 residues, 1 model selected  

> view matrix models #4,1,0,0,183.3,0,1,0,134.92,0,0,1,150.41

> select subtract #4

Nothing selected  

> ui mousemode right zoom

> ui mousemode right ""translate selected models""

> select add #4

13472 atoms, 13772 bonds, 1651 residues, 1 model selected  

> view matrix models #4,1,0,0,146.97,0,1,0,116.29,0,0,1,132.7

> ui mousemode right ""rotate selected models""

> view matrix models
> #4,-0.40748,0.80981,-0.4221,138.49,-0.82555,-0.52426,-0.20886,111.97,-0.39042,0.26336,0.88216,130.34

> view matrix models
> #4,-0.3514,0.89022,-0.28988,140,-0.78279,-0.44922,-0.43063,109.81,-0.51358,0.075593,0.85471,129.73

> view matrix models
> #4,-0.57818,0.78983,0.20465,144.44,-0.13277,0.1564,-0.97873,105.96,-0.80503,-0.59305,0.014444,120.34

> view matrix models
> #4,0.34021,0.85297,0.39585,149.03,-0.92816,0.23702,0.28696,116.67,0.15094,-0.46504,0.87233,131.88

> view matrix models
> #4,-0.40454,0.76818,0.49624,147.94,-0.90227,-0.42378,-0.079521,113.07,0.14921,-0.47991,0.86454,131.8

> ui mousemode right ""translate selected models""

> view matrix models
> #4,-0.40454,0.76818,0.49624,177.23,-0.90227,-0.42378,-0.079521,128.09,0.14921,-0.47991,0.86454,146.32

> select subtract #4

Nothing selected  

> fitmap #4 inMap #2

Fit molecule fold_2025_02_06_16_38_model_0.cif (#4) to map
cryosparc_P19_J325_005_volume_map.mrc (#2) using 13472 atoms  
average map value = 0.02812, steps = 136  
shifted from previous position = 10.7  
rotated from previous position = 5.69 degrees  
atoms outside contour = 11853, contour level = 0.080518  
  
Position of fold_2025_02_06_16_38_model_0.cif (#4) relative to
cryosparc_P19_J325_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.30333288 -0.89731410 -0.32065021 104.86768529  
0.95288411 -0.28600189 -0.10106826 146.21429275  
-0.00101659 -0.33619982 0.94179013 131.88090072  
Axis -0.12425899 -0.16891544 0.97776647  
Axis point 1.74245447 126.96959315 0.00000000  
Rotation angle (degrees) 108.89121298  
Shift along axis 91.22011994  
  

> fitmap #4 inMap #2

Fit molecule fold_2025_02_06_16_38_model_0.cif (#4) to map
cryosparc_P19_J325_005_volume_map.mrc (#2) using 13472 atoms  
average map value = 0.02812, steps = 60  
shifted from previous position = 0.0144  
rotated from previous position = 0.00463 degrees  
atoms outside contour = 11858, contour level = 0.080518  
  
Position of fold_2025_02_06_16_38_model_0.cif (#4) relative to
cryosparc_P19_J325_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.30333144 -0.89733827 -0.32058394 104.88150563  
0.95288455 -0.28601374 -0.10103054 146.21703387  
-0.00103284 -0.33612522 0.94181674 131.88426782  
Axis -0.12423914 -0.16887133 0.97777662  
Axis point 1.74802229 126.97299329 0.00000000  
Rotation angle (degrees) 108.89072283  
Shift along axis 91.23110048  
  

> fitmap #4 inMap #2

Fit molecule fold_2025_02_06_16_38_model_0.cif (#4) to map
cryosparc_P19_J325_005_volume_map.mrc (#2) using 13472 atoms  
average map value = 0.02812, steps = 64  
shifted from previous position = 0.0136  
rotated from previous position = 0.00758 degrees  
atoms outside contour = 11856, contour level = 0.080518  
  
Position of fold_2025_02_06_16_38_model_0.cif (#4) relative to
cryosparc_P19_J325_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.30332930 -0.89730138 -0.32068921 104.86857836  
0.95288527 -0.28598792 -0.10109685 146.21461903  
-0.00099890 -0.33624566 0.94177378 131.88040976  
Axis -0.12426808 -0.16894536 0.97776015  
Axis point 1.74241882 126.97242873 0.00000000  
Rotation angle (degrees) 108.89117665  
Shift along axis 91.21331198  
  

> ui mousemode right zoom

> select /A

4670 atoms, 4769 bonds, 574 residues, 1 model selected  

> color sel bychain

> color sel bypolymer

> select clear

> color bychain

> hide #4 models

> open
> /Volumes/data-4T/Projects/校外合作/SunLitao/4-BrxC/RealSpaceRefine_8/N550-dimer-
> inimod-coot-8_real_space_refined_008-coot_pro-addAGS.pdb

Chain information for N550-dimer-inimod-
coot-8_real_space_refined_008-coot_pro-addAGS.pdb #5  
---  
Chain | Description  
A B | No description available  
  

> fitmap #5 inMap #2

Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-
addAGS.pdb (#5) to map cryosparc_P19_J325_005_volume_map.mrc (#2) using 9114
atoms  
average map value = 0.1511, steps = 44  
shifted from previous position = 0.026  
rotated from previous position = 0.0664 degrees  
atoms outside contour = 1817, contour level = 0.080518  
  
Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-
addAGS.pdb (#5) relative to cryosparc_P19_J325_005_volume_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.72712412 0.68158076 0.08208640 125.63010234  
-0.67470218 -0.73157276 0.09786864 348.44159648  
0.12675756 0.01577878 0.99180822 -42.97175111  
Axis -0.06038244 -0.03285854 -0.99763434  
Axis point 132.75002980 149.95502968 0.00000000  
Rotation angle (degrees) 137.17592669  
Shift along axis 23.83496003  
  

> fitmap #5 inMap #2

Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-
addAGS.pdb (#5) to map cryosparc_P19_J325_005_volume_map.mrc (#2) using 9114
atoms  
average map value = 0.1511, steps = 40  
shifted from previous position = 0.00859  
rotated from previous position = 0.0112 degrees  
atoms outside contour = 1822, contour level = 0.080518  
  
Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-
addAGS.pdb (#5) relative to cryosparc_P19_J325_005_volume_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.72711228 0.68157819 0.08221250 125.60398173  
-0.67471648 -0.73157932 0.09772087 348.47513943  
0.12674938 0.01558392 0.99181235 -42.93735720  
Axis -0.06041662 -0.03275953 -0.99763553  
Axis point 132.74338461 149.97389489 0.00000000  
Rotation angle (degrees) 137.17553067  
Shift along axis 23.83138321  
  

> fitmap #5 inMap #2

Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-
addAGS.pdb (#5) to map cryosparc_P19_J325_005_volume_map.mrc (#2) using 9114
atoms  
average map value = 0.1511, steps = 44  
shifted from previous position = 0.00985  
rotated from previous position = 0.0131 degrees  
atoms outside contour = 1820, contour level = 0.080518  
  
Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-
addAGS.pdb (#5) relative to cryosparc_P19_J325_005_volume_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.72712327 0.68157480 0.08214343 125.61887901  
-0.67468666 -0.73157806 0.09793600 348.42976262  
0.12684504 0.01579047 0.99179685 -42.97552523  
Axis -0.06042414 -0.03288135 -0.99763106  
Axis point 132.74221142 149.95212542 0.00000000  
Rotation angle (degrees) 137.17659352  
Shift along axis 23.82646353  
  

> hide #5 models

> show #5 models

> volume #2 color #ffffb271

> show #4 models

> hide #4 models

> show #4 models

> ui tool show Matchmaker

> hide #!2 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #5 models

> matchmaker #4/A to #5/A pairing ss

Computing secondary structure  
Parameters  
---  
Chain pairing | ss  
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 N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-
addAGS.pdb, chain A (#5) with fold_2025_02_06_16_38_model_0.cif, chain A (#4),
sequence alignment score = 2667.4  
RMSD between 296 pruned atom pairs is 1.105 angstroms; (across all 559 pairs:
7.886)  
  

> show #!2 models

> show #5 models

> select #4/B

1669 atoms, 1711 bonds, 206 residues, 1 model selected  

> select clear

> hide #5 models

> hide #!2 models

> select #4/B

1669 atoms, 1711 bonds, 206 residues, 1 model selected  


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: Z1250003LCH/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.81.2
      OS Loader Version: 11881.81.2

Software:

    System Software Overview:

      System Version: macOS 15.3 (24D60)
      Kernel Version: Darwin 24.3.0
      Time since boot: 25 days, 22 hours, 9 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Window Toolkit		can't reproduce		Tom Goddard				all	ChimeraX