Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.2-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000031128d000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000200ca22c0 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2226 in process_changes
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2228 in changes
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 77 in 
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3005 in command_trigger
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 144 in __exit__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2899 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/model_panel/tool.py", line 366 in _tree_change_cb
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.mmcif.mmcif_write (total: 53)


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{
  "uptime" : 150000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir10,1",
  "coalitionID" : 896,
  "osVersion" : {
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    "build" : "22D49",
    "releaseType" : "User"
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  "captureTime" : "2024-07-05 14:53:24.3264 +0200",
  "incident" : "BEDFEED9-CBC6-48D4-A2C4-148D48B13EB6",
  "pid" : 30221,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-07-05 14:34:13.9976 +0200",
  "procStartAbsTime" : 3573137257371,
  "procExitAbsTime" : 3600744119672,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"D82AA68D-AACC-5141-AE12-1309469013C3","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "311D3808-133C-AE77-3A0C-264C8C389551",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 2170,
  "sleepWakeUUID" : "398EFC4E-9F4D-414F-929B-18E3A8E5CAFC",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140723039453015\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffca2c74000-7ffcad740000 [170.8M] r-x\/r-x SM=COW  ...t_id=c296771b",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\n",
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140723039453015\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffca2c74000-7ffcad740000 [170.8M] r-x\/r-x SM=COW  ...t_id=c296771b",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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}
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/nezakoritnik/Desktop/PepMoV-VLP/h+RNA/PepMoVVLP-
> hRNA_P76_J163.mrc

Opened PepMoVVLP-hRNA_P76_J163.mrc as #1, grid size 350,350,350, pixel 0.95,
shown at level 1.82, step 2, values float32  

> open /Users/nezakoritnik/Desktop/PepMoV-
> VLP/h+RNA/Rigidbodyrefine6/chains_filament6_real_space_refined.pdb

Chain information for chains_filament6_real_space_refined.pdb #2  
---  
Chain | Description  
Aa Ac Ae Ag Ai Ak Am Ao Aq As Au Aw Ay Ba Bc Be Bg Bi Bk Bm Bo Bq Bs Bu Bw By
Ca Cc Ce Cg Ci Ck Cm Co Cq Cs | No description available  
Ab Ad Af Ah Aj Al An Ap Ar At Av Ax Az Bb Bd Bf Bh Bj Bl Bn Bp Br Bt Bv Bx Bz
Cb Cd Cf Ch Cj Cl Cn Cp Cr Ct | No description available  
  

> select /Aa:48-272

1803 atoms, 1839 bonds, 225 residues, 1 model selected  

> select add /Ab

1903 atoms, 1948 bonds, 230 residues, 1 model selected  

> save /Users/nezakoritnik/Desktop/PepMoV-VLP/h+RNA/Coot7/mono7.cif
> selectedOnly true relModel #2

Not saving entity_poly_seq for non-authoritative sequences  

> close #2

> set bgColor white

> volume #1 step 1

> open /Users/nezakoritnik/Desktop/PepMoV-VLP/h+RNA/Coot7/mono7.cif-coot-1.pdb

Chain information for mono7.cif-coot-1.pdb #2  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
  

> open /Users/nezakoritnik/Desktop/PepMoV-VLP/h+RNA/Coot7/mono7.cif-coot-1.pdb

Chain information for mono7.cif-coot-1.pdb #3  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
  

> select add #3

3731 atoms, 3776 bonds, 230 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-8.96,0,1,0,-29.59,0,0,1,6.6495

> view matrix models #3,1,0,0,-8.7727,0,1,0,-30.621,0,0,1,2.6952

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.97022,0.2419,0.012916,-49.647,-0.24209,0.97013,0.015734,19.694,-0.0087243,-0.018392,0.99979,7.8269

> view matrix models
> #3,0.92507,0.3797,0.0084722,-65.528,-0.37979,0.92488,0.018914,54.452,-0.0006543,-0.020714,0.99979,6.6787

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.92507,0.3797,0.0084722,-60.252,-0.37979,0.92488,0.018914,57.17,-0.0006543,-0.020714,0.99979,7.2147

> view matrix models
> #3,0.92507,0.3797,0.0084722,-60.24,-0.37979,0.92488,0.018914,57.218,-0.0006543,-0.020714,0.99979,7.2134

> ui tool show "Fit in Map"

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 164  
shifted from previous position = 5.93  
rotated from previous position = 19 degrees  
atoms outside contour = 2672, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75101400 0.66028519 0.00120025 -68.42797479  
-0.66028389 0.75101493 -0.00132368 151.48408351  
-0.00177541 0.00020159 0.99999840 4.29256866  
Axis 0.00115501 0.00225331 -0.99999679  
Axis point 166.66143888 166.47304328 0.00000000  
Rotation angle (degrees) 41.32173843  
Shift along axis -4.03024918  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0228  
rotated from previous position = 0.0135 degrees  
atoms outside contour = 2670, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75088704 0.66042943 0.00127376 -68.41810323  
-0.66042833 0.75088811 -0.00121004 151.52219961  
-0.00175560 0.00006737 0.99999846 4.32100760  
Axis 0.00096710 0.00229347 -0.99999690  
Axis point 166.65830049 166.45372558 0.00000000  
Rotation angle (degrees) 41.33274600  
Shift along axis -4.03964910  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 40  
shifted from previous position = 0.0211  
rotated from previous position = 0.0125 degrees  
atoms outside contour = 2671, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75100590 0.66029437 0.00121640 -68.42981385  
-0.66029308 0.75100686 -0.00131927 151.49008012  
-0.00178463 0.00018760 0.99999839 4.29922713  
Axis 0.00114105 0.00227249 -0.99999677  
Axis point 166.66483108 166.47691712 0.00000000  
Rotation angle (degrees) 41.32244086  
Shift along axis -4.03303541  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.00924  
rotated from previous position = 0.00526 degrees  
atoms outside contour = 2670, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75098801 0.66031468 0.00123740 -68.42432101  
-0.66031354 0.75098902 -0.00123407 151.48588405  
-0.00174415 0.00010970 0.99999847 4.30771342  
Axis 0.00101751 0.00225767 -0.99999693  
Axis point 166.65343619 166.46444798 0.00000000  
Rotation angle (degrees) 41.32398726  
Shift along axis -4.03531797  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0115  
rotated from previous position = 0.00871 degrees  
atoms outside contour = 2671, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75093443 0.66037549 0.00130040 -68.42301415  
-0.66037414 0.75093554 -0.00134633 151.52656397  
-0.00186560 0.00015225 0.99999825 4.32863478  
Axis 0.00113464 0.00239711 -0.99999648  
Axis point 166.68443579 166.47162420 0.00000000  
Rotation angle (degrees) 41.32864176  
Shift along axis -4.04302843  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0266  
rotated from previous position = 0.00673 degrees  
atoms outside contour = 2673, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75098761 0.66031513 0.00124527 -68.43968271  
-0.66031390 0.75098863 -0.00128065 151.49251282  
-0.00178081 0.00013949 0.99999840 4.30445120  
Axis 0.00107535 0.00229138 -0.99999680  
Axis point 166.65466086 166.48781759 0.00000000  
Rotation angle (degrees) 41.32402507  
Shift along axis -4.03090621  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0252  
rotated from previous position = 0.00791 degrees  
atoms outside contour = 2669, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75091017 0.66040313 0.00126964 -68.41949773  
-0.66040202 0.75091124 -0.00121199 151.51435591  
-0.00175379 0.00007162 0.99999846 4.31964376  
Axis 0.00097184 0.00228908 -0.99999691  
Axis point 166.65784472 166.45642667 0.00000000  
Rotation angle (degrees) 41.33073876  
Shift along axis -4.03929493  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.00276  
rotated from previous position = 0.0035 degrees  
atoms outside contour = 2668, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75087069 0.66044803 0.00127060 -68.41946227  
-0.66044694 0.75087176 -0.00119954 151.53126740  
-0.00174629 0.00006153 0.99999847 4.31919357  
Axis 0.00095470 0.00228397 -0.99999694  
Axis point 166.66202623 166.45670568 0.00000000  
Rotation angle (degrees) 41.33416368  
Shift along axis -4.03840847  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0172  
rotated from previous position = 0.00956 degrees  
atoms outside contour = 2671, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75096676 0.66033881 0.00125647 -68.43372538  
-0.66033758 0.75096780 -0.00127992 151.50127489  
-0.00178875 0.00013149 0.99999839 4.31041735  
Axis 0.00106870 0.00230579 -0.99999677  
Axis point 166.65973757 166.48003500 0.00000000  
Rotation angle (degrees) 41.32583326  
Shift along axis -4.03420821  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0148  
rotated from previous position = 0.0063 degrees  
atoms outside contour = 2670, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75091517 0.66039745 0.00127220 -68.42207733  
-0.66039635 0.75091624 -0.00120425 151.51123673  
-0.00175060 0.00006413 0.99999847 4.31952396  
Axis 0.00096031 0.00228862 -0.99999692  
Axis point 166.65469007 166.45938688 0.00000000  
Rotation angle (degrees) 41.33030503  
Shift along axis -4.03846555  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.00237  
rotated from previous position = 0.00218 degrees  
atoms outside contour = 2668, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75091650 0.66039597 0.00125372 -68.41817363  
-0.66039493 0.75091755 -0.00117111 151.50774612  
-0.00171484 0.00005145 0.99999853 4.31411418  
Axis 0.00092563 0.00224756 -0.99999705  
Axis point 166.65231049 166.45282938 0.00000000  
Rotation angle (degrees) 41.33018766  
Shift along axis -4.03690879  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0157  
rotated from previous position = 0.0107 degrees  
atoms outside contour = 2671, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75100634 0.66029383 0.00124066 -68.43131936  
-0.66029257 0.75100735 -0.00129908 151.48819246  
-0.00178952 0.00015642 0.99999839 4.30622617  
Axis 0.00110216 0.00229456 -0.99999676  
Axis point 166.66183023 166.47832789 0.00000000  
Rotation angle (degrees) 41.32240091  
Shift along axis -4.03403554  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.016  
rotated from previous position = 0.00845 degrees  
atoms outside contour = 2668, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75092643 0.66038467 0.00126291 -68.41944815  
-0.66038355 0.75092748 -0.00121796 151.50851382  
-0.00175267 0.00008059 0.99999846 4.31743213  
Axis 0.00098317 0.00228319 -0.99999691  
Axis point 166.65759733 166.45674307 0.00000000  
Rotation angle (degrees) 41.32932922  
Shift along axis -4.03876351  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.00254  
rotated from previous position = 0.00602 degrees  
atoms outside contour = 2669, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75086915 0.66044975 0.00128218 -68.42198192  
-0.66044853 0.75087024 -0.00127433 151.54295658  
-0.00180439 0.00011004 0.99999837 4.32241927  
Axis 0.00104805 0.00233671 -0.99999672  
Axis point 166.67606363 166.46519549 0.00000000  
Rotation angle (degrees) 41.33430135  
Shift along axis -4.04000224  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0174  
rotated from previous position = 0.0127 degrees  
atoms outside contour = 2671, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75101425 0.66028481 0.00125054 -68.43389438  
-0.66028359 0.75101528 -0.00127672 151.48162996  
-0.00178217 0.00013312 0.99999840 4.30845978  
Axis 0.00106760 0.00229651 -0.99999679  
Axis point 166.65542364 166.48030026 0.00000000  
Rotation angle (degrees) 41.32171289  
Shift along axis -4.03362646  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0172  
rotated from previous position = 0.00864 degrees  
atoms outside contour = 2668, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75092349 0.66038800 0.00126446 -68.41954578  
-0.66038689 0.75092455 -0.00121639 151.50958042  
-0.00175281 0.00007838 0.99999846 4.31791702  
Axis 0.00098031 0.00228446 -0.99999691  
Axis point 166.65761155 166.45681378 0.00000000  
Rotation angle (degrees) 41.32958391  
Shift along axis -4.03885830  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.00246  
rotated from previous position = 0.00585 degrees  
atoms outside contour = 2669, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75086769 0.66045141 0.00128210 -68.42174572  
-0.66045019 0.75086878 -0.00127099 151.54304419  
-0.00180211 0.00010758 0.99999837 4.32240305  
Axis 0.00104365 0.00233492 -0.99999673  
Axis point 166.67560822 166.46464328 0.00000000  
Rotation angle (degrees) 41.33442730  
Shift along axis -4.03995619  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0175  
rotated from previous position = 0.013 degrees  
atoms outside contour = 2671, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75101520 0.66028373 0.00124710 -68.43326684  
-0.66028250 0.75101623 -0.00128423 151.48236446  
-0.00178454 0.00014104 0.99999840 4.30758941  
Axis 0.00107928 0.00229571 -0.99999678  
Axis point 166.65717176 166.47996883 0.00000000  
Rotation angle (degrees) 41.32163044  
Shift along axis -4.03367528  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.017  
rotated from previous position = 0.00866 degrees  
atoms outside contour = 2668, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75092620 0.66038492 0.00126315 -68.41944266  
-0.66038380 0.75092726 -0.00121806 151.50869998  
-0.00175292 0.00008051 0.99999846 4.31752144  
Axis 0.00098319 0.00228356 -0.99999691  
Axis point 166.65774525 166.45678279 0.00000000  
Rotation angle (degrees) 41.32934879  
Shift along axis -4.03879823  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.00246  
rotated from previous position = 0.00653 degrees  
atoms outside contour = 2669, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75086869 0.66045027 0.00128594 -68.42242501  
-0.66044902 0.75086978 -0.00128808 151.54522325  
-0.00181629 0.00011789 0.99999834 4.32353620  
Axis 0.00106440 0.00234856 -0.99999668  
Axis point 166.67874191 166.46676218 0.00000000  
Rotation angle (degrees) 41.33434174  
Shift along axis -4.04043684  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0179  
rotated from previous position = 0.0126 degrees  
atoms outside contour = 2671, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75101184 0.66028754 0.00125856 -68.43546419  
-0.66028635 0.75101288 -0.00125968 151.48004632  
-0.00177694 0.00011502 0.99999841 4.31043680  
Axis 0.00104098 0.00229861 -0.99999682  
Axis point 166.65138383 166.48123810 0.00000000  
Rotation angle (degrees) 41.32192098  
Shift along axis -4.03346936  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.018  
rotated from previous position = 0.00877 degrees  
atoms outside contour = 2669, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75091572 0.66039683 0.00126750 -68.41960351  
-0.66039572 0.75091679 -0.00121321 151.51218300  
-0.00175298 0.00007397 0.99999846 4.31886311  
Axis 0.00097455 0.00228686 -0.99999691  
Axis point 166.65745740 166.45661342 0.00000000  
Rotation angle (degrees) 41.33025770  
Shift along axis -4.03904035  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.00263  
rotated from previous position = 0.00394 degrees  
atoms outside contour = 2668, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75087037 0.66044839 0.00126955 -68.41960986  
-0.66044728 0.75087144 -0.00121184 151.53306177  
-0.00175363 0.00007147 0.99999846 4.31886208  
Axis 0.00097154 0.00228873 -0.99999691  
Axis point 166.66424855 166.45765297 0.00000000  
Rotation angle (degrees) 41.33419189  
Shift along axis -4.03850351  
  

> fitmap sel inMap #1

Fit molecule mono7.cif-coot-1.pdb (#3) to map PepMoVVLP-hRNA_P76_J163.mrc (#1)
using 3731 atoms  
average map value = 1.236, steps = 28  
shifted from previous position = 0.0171  
rotated from previous position = 0.0107 degrees  
atoms outside contour = 2671, contour level = 1.8153  
  
Position of mono7.cif-coot-1.pdb (#3) relative to PepMoVVLP-hRNA_P76_J163.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.75098629 0.66031661 0.00125527 -68.43383549  
-0.66031539 0.75098732 -0.00127526 151.49271115  
-0.00178476 0.00012883 0.99999840 4.30998901  
Axis 0.00106319 0.00230194 -0.99999679  
Axis point 166.65728769 166.47998168 0.00000000  
Rotation angle (degrees) 41.32413896  
Shift along axis -4.03400568  
  

> open /Users/nezakoritnik/Desktop/PepMoV-VLP/h+RNA/Coot7/mono7.cif-coot-1.pdb

Chain information for mono7.cif-coot-1.pdb #4  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
  

> select add #4

7462 atoms, 7552 bonds, 460 residues, 2 models selected  

> select subtract #4

3731 atoms, 3776 bonds, 230 residues, 1 model selected  

> select subtract #3

Nothing selected  


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.2
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
      Model Number: Z128000N6ZE/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2 (22D49)
      Kernel Version: Darwin 22.3.0
      Time since boot: 7 days, 18 hours, 6 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
        HP E243i:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    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: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9