id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16563	Graphics crash, macOS 15.2, Radeon Pro Vega 56	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.2-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics.
Fatal Python error: Aborted

Current thread 0x00007ff85e7134c0 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 202 in draw
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.graphics._graphics, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath (total: 50)


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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: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/navid/Downloads/cryosparc_P4_J1551_005_volume_map_sharp.mrc

Opened cryosparc_P4_J1551_005_volume_map_sharp.mrc as #1, grid size
480,480,480, pixel 0.663, shown at level 0.0611, step 2, values float32  

> volume #0-100 fastEncloseVolume 1250000

> volume #0-100 fastEncloseVolume 50000

> volume #0-100 step 1 fastEncloseVolume 50000

> volume #1 level 0.1235

> volume #0-100 step 1 fastEncloseVolume 40000

> open /Users/navid/Downloads/emd_23375.map

Opened emd_23375.map as #2, grid size 300,300,300, pixel 1.03, shown at level
0.118, step 2, values float32  

> open /Users/navid/Downloads/emd_23374.map

Opened emd_23374.map as #3, grid size 300,300,300, pixel 1.03, shown at level
0.216, step 2, values float32  

> open /Users/navid/Downloads/emd_23372.map

Opened emd_23372.map as #4, grid size 300,300,300, pixel 1.03, shown at level
0.121, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> ui dockable false ""Model Panel""

> ui dockable false Log

> ui autostart false Log

> ui autostart true ""Volume Viewer""

> hide #!1 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!4 models

> hide #!2 models

> volume #4 level 0.3757

> show #!3 models

> show #!2 models

> hide #!4 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!3 models

> show #!4 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #4 level 0.2909

> open /Users/navid/Downloads/cryosparc_P4_J1503_004_volume_map.mrc

Opened cryosparc_P4_J1503_004_volume_map.mrc as #5, grid size 480,480,480,
pixel 0.663, shown at level 0.0457, step 2, values float32  

> open /Users/navid/Downloads/cryosparc_P4_J1507_005_volume_map.mrc

Opened cryosparc_P4_J1507_005_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.663, shown at level 0.0537, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> close #1

> close #2

> close #3

> close #4

> close #5

> close #6

> open /Users/navid/Downloads/emd_23374.map format ccp4

Opened emd_23374.map as #1, grid size 300,300,300, pixel 1.03, shown at level
0.216, step 2, values float32  

> open /Users/navid/Downloads/emd_23372.map
> /Users/navid/Downloads/emd_23374.map /Users/navid/Downloads/emd_23375.map

Opened emd_23372.map as #2.1, grid size 300,300,300, pixel 1.03, shown at
level 0.121, step 2, values float32  
Opened emd_23374.map as #2.2, grid size 300,300,300, pixel 1.03, shown at
level 0.216, step 2, values float32  
Opened emd_23375.map as #2.3, grid size 300,300,300, pixel 1.03, shown at
level 0.118, step 2, values float32  

> close #1

> volume #0-100 step 1 fastEncloseVolume 40000

> view center

Expected an objects specifier or a view name or a keyword  

> center

Unknown command: center  

> view orient

> turn x, 90

Expected an axis vector or a keyword  

> turn x 90

> turn y, 1

Expected an axis vector or a keyword  

> turn y 1

> ui tool show ""Side View""

> ui autostart true ""Side View""

> ui dockable false ""Side View""

> turn y 1

> volume #0-100 step 1 fastEncloseVolume 60000

> volume #0-100 step 1 fastEncloseVolume 70000

> save /Users/navid/Desktop/img1.png

> save /Users/navid/Desktop/img2.png

> save /Users/navid/Desktop/img3.png

> save /Users/navid/Desktop/img4.png

> volume #0-100 step 1 fastEncloseVolume 100000

> turn y 1

> open /Users/navid/Downloads/cryosparc_P4_J1574_004_volume_map_sharp.mrc

Opened cryosparc_P4_J1574_004_volume_map_sharp.mrc as #1, grid size
480,480,480, pixel 0.663, shown at level 0.0567, step 2, values float32  

> close #2.1

> close #2.2

> close #2.3

> volume #0-100 step 1 fastEncloseVolume 100000

> volume #0-100 step 1 fastEncloseVolume 30000

> volume #0-100 step 1 fastEncloseVolume 40000

> open /Users/navid/Downloads/cryosparc_P4_J1575_004_volume_map_sharp.mrc

Opened cryosparc_P4_J1575_004_volume_map_sharp.mrc as #3, grid size
480,480,480, pixel 0.663, shown at level 0.0571, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> open /Users/navid/Downloads/cryosparc_P4_J1571_002_volume_map_sharp.mrc

Opened cryosparc_P4_J1571_002_volume_map_sharp.mrc as #4, grid size
480,480,480, pixel 0.663, shown at level 0.058, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> open /Users/navid/Downloads/cryosparc_P4_J1581_005_volume_map_sharp.mrc

Opened cryosparc_P4_J1581_005_volume_map_sharp.mrc as #5, grid size
480,480,480, pixel 0.663, shown at level 0.0641, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> close #1

> close #3

> close #4

> open /Users/navid/Downloads/cryosparc_P4_J1582_005_volume_map_sharp.mrc

Opened cryosparc_P4_J1582_005_volume_map_sharp.mrc as #1, grid size
480,480,480, pixel 0.663, shown at level 0.0672, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> fitmap #1 #5

Missing required ""in_map"" argument  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J1582_005_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137090 points  
correlation = 0.9614, correlation about mean = 0.7312, overlap = 1.049e+04  
steps = 52, shift = 0.25, angle = 0.201 degrees  
  
Position of cryosparc_P4_J1582_005_volume_map_sharp.mrc (#1) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999740 0.00221129 -0.00055570 -0.20578402  
-0.00221276 0.99999403 -0.00265571 0.89265278  
0.00054983 0.00265693 0.99999632 -0.29618172  
Axis 0.75880415 -0.15790337 -0.63188827  
Axis point 0.00000000 138.08007692 329.27815751  
Rotation angle (degrees) 0.20057373  
Shift along axis -0.10994889  
  

> open /Users/navid/Downloads/cryosparc_P4_J1583_005_volume_map_sharp.mrc

Opened cryosparc_P4_J1583_005_volume_map_sharp.mrc as #3, grid size
480,480,480, pixel 0.663, shown at level 0.0619, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> fitmap #3 inMap #5

Fit map cryosparc_P4_J1583_005_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137411 points  
correlation = 0.9618, correlation about mean = 0.7441, overlap = 8800  
steps = 60, shift = 0.185, angle = 0.135 degrees  
  
Position of cryosparc_P4_J1583_005_volume_map_sharp.mrc (#3) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999896 -0.00123205 0.00075254 0.13429319  
0.00123346 0.99999749 -0.00187193 0.26362467  
-0.00075023 0.00187286 0.99999796 -0.24451352  
Axis 0.79192955 0.31779844 0.52139404  
Axis point 0.00000000 148.13688523 129.99656920  
Rotation angle (degrees) 0.13546718  
Shift along axis 0.06264236  
  

> view center

Expected an objects specifier or a view name or a keyword  

> orient

Unknown command: orient  

> view orient

> center

Unknown command: center  

> open /Users/navid/Downloads/cryosparc_P4_J1584_005_volume_map_sharp.mrc

Opened cryosparc_P4_J1584_005_volume_map_sharp.mrc as #4, grid size
480,480,480, pixel 0.663, shown at level 0.0617, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> fitmap #4 inMap #5

Fit map cryosparc_P4_J1584_005_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137561 points  
correlation = 0.9571, correlation about mean = 0.7266, overlap = 9193  
steps = 40, shift = 0.152, angle = 0.158 degrees  
  
Position of cryosparc_P4_J1584_005_volume_map_sharp.mrc (#4) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999678 -0.00180904 -0.00177994 0.67938840  
0.00180714 0.99999780 -0.00106832 -0.12259903  
0.00178186 0.00106510 0.99999785 -0.55841434  
Axis 0.38748082 -0.64690840 0.65678622  
Axis point 76.96784848 380.59739173 0.00000000  
Rotation angle (degrees) 0.15773204  
Shift along axis -0.02419853  
  

> open /Users/navid/Downloads/cryosparc_P4_J1585_004_volume_map_sharp.mrc

Opened cryosparc_P4_J1585_004_volume_map_sharp.mrc as #6, grid size
480,480,480, pixel 0.663, shown at level 0.0661, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> fitmap #6 inMap #5

Fit map cryosparc_P4_J1585_004_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137001 points  
correlation = 0.9614, correlation about mean = 0.7297, overlap = 1.066e+04  
steps = 60, shift = 0.26, angle = 0.139 degrees  
  
Position of cryosparc_P4_J1585_004_volume_map_sharp.mrc (#6) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999708 0.00173710 -0.00168222 -0.05448146  
-0.00173734 0.99999848 -0.00013765 0.36874115  
0.00168198 0.00014057 0.99999858 -0.04395357  
Axis 0.05743252 -0.69446927 -0.71722656  
Axis point 121.21161759 24.03969426 0.00000000  
Rotation angle (degrees) 0.13877819  
Shift along axis -0.22768374  
  

> open /Users/navid/Downloads/cryosparc_P4_J1586_005_volume_map_sharp.mrc

Opened cryosparc_P4_J1586_005_volume_map_sharp.mrc as #7, grid size
480,480,480, pixel 0.663, shown at level 0.0634, step 2, values float32  

> fitmap #7 inMap #5

Fit map cryosparc_P4_J1586_005_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137843 points  
correlation = 0.8484, correlation about mean = 0.7893, overlap = 1731  
steps = 72, shift = 0.057, angle = 0.188 degrees  
  
Position of cryosparc_P4_J1586_005_volume_map_sharp.mrc (#7) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999548 -0.00200484 -0.00224260 0.70273530  
0.00200187 0.99999712 -0.00132601 -0.07020167  
0.00224525 0.00132151 0.99999661 -0.61680949  
Axis 0.40278881 -0.68277396 0.60957436  
Axis point 262.98332074 0.00000000 320.90985491  
Rotation angle (degrees) 0.18830222  
Shift along axis -0.04500546  
  

> volume #0-100 step 1 fastEncloseVolume 40000

> open /Users/navid/Downloads/cryosparc_P4_J1587_005_volume_map_sharp.mrc

Opened cryosparc_P4_J1587_005_volume_map_sharp.mrc as #8, grid size
480,480,480, pixel 0.663, shown at level 0.0629, step 2, values float32  

> fitmap #8 inMap #5

Fit map cryosparc_P4_J1587_005_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137900 points  
correlation = 0.855, correlation about mean = 0.7941, overlap = 1728  
steps = 52, shift = 0.153, angle = 0.216 degrees  
  
Position of cryosparc_P4_J1587_005_volume_map_sharp.mrc (#8) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999354 -0.00323644 -0.00156155 0.73888787  
0.00323463 0.99999410 -0.00115875 -0.26275230  
0.00156529 0.00115369 0.99999811 -0.56893009  
Axis 0.30629197 -0.41416289 0.85711979  
Axis point 101.20019342 242.53362032 0.00000000  
Rotation angle (degrees) 0.21628588  
Shift along axis -0.15250357  
  

> volume #0-100 step 1 fastEncloseVolume 40000

> open /Users/navid/Downloads/cryosparc_P4_J1588_004_volume_map_sharp.mrc

Opened cryosparc_P4_J1588_004_volume_map_sharp.mrc as #9, grid size
480,480,480, pixel 0.663, shown at level 0.065, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> open /Users/navid/Downloads/cryosparc_P4_J1589_005_volume_map_sharp.mrc

Opened cryosparc_P4_J1589_005_volume_map_sharp.mrc as #10, grid size
480,480,480, pixel 0.663, shown at level 0.0631, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> open /Users/navid/Downloads/cryosparc_P4_J1590_005_volume_map_sharp.mrc

Opened cryosparc_P4_J1590_005_volume_map_sharp.mrc as #11, grid size
480,480,480, pixel 0.663, shown at level 0.0606, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> open /Users/navid/Downloads/cryosparc_P4_J1591_006_volume_map_sharp.mrc

Opened cryosparc_P4_J1591_006_volume_map_sharp.mrc as #12, grid size
480,480,480, pixel 0.663, shown at level 0.0606, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> open /Users/navid/Downloads/cryosparc_P4_J1592_005_volume_map_sharp.mrc

Opened cryosparc_P4_J1592_005_volume_map_sharp.mrc as #13, grid size
480,480,480, pixel 0.663, shown at level 0.0609, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> set bgColor white

> lighting soft

> open /Users/navid/Downloads/emd_36410.map

Opened emd_36410.map as #14, grid size 240,240,240, pixel 0.93, shown at level
0.0133, step 1, values float32  

> close #2#1,3-13

> volume #0-100 step 1 fastEncloseVolume 40000

> view orient

> close #14

> open /Users/navid/Downloads/emd_36417.map

Opened emd_36417.map as #1, grid size 240,240,240, pixel 0.93, shown at level
0.0155, step 1, values float32  

> open /Users/navid/Downloads/emd_38133.map

Opened emd_38133.map as #2, grid size 240,240,240, pixel 0.93, shown at level
0.0132, step 1, values float32  

> open /Users/navid/Downloads/emd_36410.map

Opened emd_36410.map as #3, grid size 240,240,240, pixel 0.93, shown at level
0.0133, step 1, values float32  

> volume #0-100 step 1 fastEncloseVolume 40000

> turn x, 90

Expected an axis vector or a keyword  

> turn x 90

> turn y 1

> volume #3 level 0.01603

> volume #2 level 0.01438

> volume #1 level 0.01247

> open /Users/navid/Downloads/cryosparc_P4_J1602_map.mrc

Opened cryosparc_P4_J1602_map.mrc as #4, grid size 240,240,240, pixel 0.93,
shown at level 0.0106, step 1, values float32  

> close #1

> close #2

> close #3

> volume #0-100 step 1 fastEncloseVolume 100000

> volume #0-100 step 1 fastEncloseVolume 1000000

> volume #0-100 step 1 fastEncloseVolume 500000

> volume #0-100 step 1 fastEncloseVolume 400000

> volume #0-100 step 1 fastEncloseVolume 300000

> volume #0-100 step 1 fastEncloseVolume 200000

> volume #0-100 step 1 fastEncloseVolume 150000

> open /Users/navid/Downloads/cryosparc_P4_J1608_map.mrc

Opened cryosparc_P4_J1608_map.mrc as #1, grid size 240,240,240, pixel 0.93,
shown at level 0.00768, step 1, values float32  

> open /Users/navid/Downloads/cryosparc_P4_J1610_map.mrc

Opened cryosparc_P4_J1610_map.mrc as #2, grid size 480,480,480, pixel 0.663,
shown at level 0.0458, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 150000

> volume #0-100 step 1 fastEncloseVolume 50000

> select #1

2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #1,1,0,0,45.624,0,1,0,42.43,0,0,1,0.91972

> view matrix models #1,1,0,0,45.858,0,1,0,50.433,0,0,1,47.466

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.42352,0.89281,-0.15334,27.507,0.73844,-0.2422,0.62932,37.085,0.52473,-0.37977,-0.76187,226.05

> view matrix models
> #1,0.2591,0.94026,0.22086,-0.80315,0.96576,-0.24912,-0.072387,90.056,-0.013042,0.23205,-0.97262,241.08

> fitmap #1 inMap #2

Fit map cryosparc_P4_J1608_map.mrc in map cryosparc_P4_J1610_map.mrc using
62160 points  
correlation = 0.6879, correlation about mean = 0.1059, overlap = 131  
steps = 204, shift = 6.91, angle = 12.9 degrees  
  
Position of cryosparc_P4_J1608_map.mrc (#1) relative to
cryosparc_P4_J1610_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.16103600 0.98572515 0.04912589 25.40710208  
0.98589977 -0.16295955 0.03802427 62.60063168  
0.04548701 0.04230993 -0.99806854 264.61475018  
Axis 0.76191662 0.64693069 0.03104417  
Axis point 0.00000000 20.27170290 131.80690150  
Rotation angle (degrees) 179.83886000  
Shift along axis 68.07110761  
  

> show #!4 models

> hide #!4 models

> ui mousemode right ""rotate selected models""

> select clear

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> turn x 90

> show #!4 models

> hide #!2 models

> show #!2 models

> hide #!4 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> turn y 90

> turn y 1

> turn y -1

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> open /Users/navid/Downloads/cryosparc_P4_J1612_map.mrc

Opened cryosparc_P4_J1612_map.mrc as #3, grid size 480,480,480, pixel 0.663,
shown at level 0.0459, step 2, values float32  

> volume #0-100 step 1 fastEncloseVolume 50000


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

OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro Vega 56 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: iMac Pro
      Model Identifier: iMacPro1,1
      Processor Name: 8-Core Intel Xeon W
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 1 MB
      L3 Cache: 11 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.12093.0.0,0)
      OS Loader Version: 582~2898

Software:

    System Software Overview:

      System Version: macOS 15.2 (24C101)
      Kernel Version: Darwin 24.2.0
      Time since boot: 1 hour

Graphics/Displays:

    Radeon Pro Vega 56:

      Chipset Model: Radeon Pro Vega 56
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6867
      Revision ID: 0x0000
      ROM Revision: 113-D0500D-114
      VBIOS Version: 113-D05001A1XL-018
      Option ROM Version: 113-D05001A1XL-018
      EFI Driver Version: 01.01.114
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          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		Graphics		nonchimerax						all	ChimeraX