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Opened 5 hours ago
#20364 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-13.7.6-x86_64-i386-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 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. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00007ff85e47aa00 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics (total: 46)
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{
"uptime" : 1000000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 228799,
"osVersion" : {
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"build" : "22H625",
"releaseType" : "User"
},
"captureTime" : "2026-05-18 18:15:52.5712 -0400",
"incident" : "A68BD40A-6521-4073-96D1-BCED6D9FDF18",
"pid" : 95300,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-05-18 17:02:51.6444 -0400",
"procStartAbsTime" : 1058154934800215,
"procExitAbsTime" : 1062534836837367,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"ED384F36-3934-52A1-9ECF-177702680592","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "78B83D24-5FA1-CEDC-7626-A65A78D8D801",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 28149,
"bridgeVersion" : {"build":"22P5072","train":"9.5"},
"sleepWakeUUID" : "AF1F639D-4B03-4610-8ABF-C9E407315251",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4499148800\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10c2b9000-10c2bd000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":95300},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4499148800\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10c2b9000-10c2bd000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"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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"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=4.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 1296K 4 \nCG image 388K 33 \nColorSync 264K 30 \nCoreAnimation 468K 63 \nCoreGraphics 16K 3 \nCoreUI image data 2848K 44 \nFoundation 40K 2 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 1.6G 417 \nMALLOC guard page 48K 10 \nMALLOC_MEDIUM (reserved) 1.5G 16 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 132K 33 \nStack 197.3M 34 \nStack Guard 56.0M 1 \nVM_ALLOCATE 241.3M 225 \nVM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 44.2M 786 \n__DATA_CONST 62.7M 486 \n__DATA_DIRTY 1865K 242 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 200.5M 138 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 1.0G 788 \ndyld private memory 340K 4 \nmapped file 253.8M 60 \nshared memory 3500K 26 \n=========== ======= ======= \nTOTAL 5.8G 3467 \nTOTAL, minus reserved VM space 3.7G 3467 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "7274def9926329cd5d888339540b12fe22d0b0fe",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6410af69ed1e1e7ab93ed169",
"factorPackIds" : {
},
"deploymentId" : 240000011
},
{
"rolloutId" : "62c73fd17cce0d1b0bcb8a02",
"factorPackIds" : {
},
"deploymentId" : 240000212
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
warning | Registration file '/Users/joanapaulino/Library/Application Support/ChimeraX/registration' has expired
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P44_J80_volume_map.mrc
Opened cryosparc_P44_J80_volume_map.mrc as #1, grid size 128,128,128, pixel
2.66, shown at level 0.699, step 1, values float32
> close #1
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P44_J146_class_03_02800_volume.mrc
Opened cryosparc_P44_J146_class_03_02800_volume.mrc as #1, grid size
128,128,128, pixel 2.66, shown at level 1.24, step 1, values float32
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P44_J157_008_volume_map.mrc
Opened cryosparc_P44_J157_008_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.664, shown at level 0.052, step 2, values float32
> hide #!1 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P44_J156_class_01_00131_volume.mrc
Opened cryosparc_P44_J156_class_01_00131_volume.mrc as #3, grid size
120,120,120, pixel 2.83, shown at level 0.396, step 1, values float32
> volume #3 level 0.22
> hide #!3 models
> hide #!2 models
> show #!1 models
> show #!3 models
> select add #3
2 models selected
> select subtract #3
Nothing selected
> select add #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.76764,0.49743,0.40409,149.8,-0.34151,0.21604,-0.91471,348.65,-0.5423,-0.84017,0.004035,406.61
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.76764,0.49743,0.40409,136.73,-0.34151,0.21604,-0.91471,337.36,-0.5423,-0.84017,0.004035,388.4
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.056864,-0.031186,0.99789,-19.747,-0.99419,0.089741,0.059457,300.87,-0.091406,-0.99548,-0.025902,342.21
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.056864,-0.031186,0.99789,-14.956,-0.99419,0.089741,0.059457,292.31,-0.091406,-0.99548,-0.025902,352.31
> view matrix models
> #1,0.056864,-0.031186,0.99789,-2.4299,-0.99419,0.089741,0.059457,294.75,-0.091406,-0.99548,-0.025902,353.56
> select subtract #1
Nothing selected
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit map cryosparc_P44_J156_class_01_00131_volume.mrc in map
cryosparc_P44_J146_class_03_02800_volume.mrc using 29267 points
correlation = 0.924, correlation about mean = 0.7179, overlap = 3.266e+04
steps = 96, shift = 14.4, angle = 11 degrees
Position of cryosparc_P44_J156_class_01_00131_volume.mrc (#3) relative to
cryosparc_P44_J146_class_03_02800_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.15685097 -0.95582068 -0.24860533 336.32467441
-0.07244813 0.23990740 -0.96808869 293.79482062
0.98496145 0.16985664 -0.03161771 -27.10125608
Axis 0.60000377 -0.65042203 0.46577533
Axis point 318.17453914 0.00000000 278.37985712
Rotation angle (degrees) 108.50755333
Shift along axis -1.91764846
> color #3 #b2ffff78 models
> set bgColor white
> lighting full
> graphics silhouettes true
> volume #1 level 0.9076
> volume #3 level 0.4183
> hide #!1 models
> show #!1 models
> volume #3 level 0.197
> hide #!3 models
> show #!3 models
> color #3 #b2ffffff models
> color #1 #b2b2b26b models
> color #1 #b2b2b255 models
> color #1 #b2b2b254 models
> color #1 #80808054 models
> color #1 #80808047 models
> color #1 #80808094 models
> color #1 grey models
> color #1 #8080807e models
> color #1 #b8b8b87e models
> color #1 #b8b8b8ff models
> show #!2 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit map cryosparc_P44_J156_class_01_00131_volume.mrc in map
cryosparc_P44_J157_008_volume_map.mrc using 33107 points
correlation = 0.943, correlation about mean = 0.868, overlap = 2430
steps = 216, shift = 15, angle = 11.1 degrees
Position of cryosparc_P44_J156_class_01_00131_volume.mrc (#3) relative to
cryosparc_P44_J157_008_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99998733 0.00019387 0.00503036 -0.93122760
-0.00018972 0.99999964 -0.00082555 -0.16517579
-0.00503052 0.00082459 0.99998701 0.54028535
Axis 0.16173842 0.98611716 -0.03759824
Axis point 104.45543584 0.00000000 174.65158920
Rotation angle (degrees) 0.29228209
Shift along axis -0.33381174
> color #3 #b2ffff84 models
> color #3 #b2ffff85 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!2 models
> fitmap #1 inMap #2
Fit map cryosparc_P44_J146_class_03_02800_volume.mrc in map
cryosparc_P44_J157_008_volume_map.mrc using 30976 points
correlation = 0.8508, correlation about mean = 0.6302, overlap = 5576
steps = 260, shift = 16.9, angle = 11.4 degrees
Position of cryosparc_P44_J146_class_03_02800_volume.mrc (#1) relative to
cryosparc_P44_J157_008_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.18627340 -0.05636170 0.98088000 -10.55580626
-0.95351149 0.23034493 0.19431170 251.97952476
-0.23689248 -0.97147546 -0.01083440 361.92767640
Axis -0.61045957 0.63768147 -0.46978874
Axis point 323.44910964 0.00000000 280.89786916
Rotation angle (degrees) 107.28398746
Shift along axis -2.90298074
> show #!2 models
> hide #!3 models
> color #1 #b8b8b89d models
> color #1 #b8b8b871 models
> color #1 #b8b8b870 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P44_J80_volume_map.mrc
Opened cryosparc_P44_J80_volume_map.mrc as #4, grid size 128,128,128, pixel
2.66, shown at level 0.699, step 1, values float32
> close #4
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P44_J146_class_03_02800_volume.mrc
Opened cryosparc_P44_J146_class_03_02800_volume.mrc as #4, grid size
128,128,128, pixel 2.66, shown at level 1.24, step 1, values float32
> ui tool show "Fit in Map"
> fitmap #4 inMap #2
Fit map cryosparc_P44_J146_class_03_02800_volume.mrc in map
cryosparc_P44_J157_008_volume_map.mrc using 20964 points
correlation = 0.7234, correlation about mean = 0.2516, overlap = 3521
steps = 1088, shift = 6.93, angle = 101 degrees
Position of cryosparc_P44_J146_class_03_02800_volume.mrc (#4) relative to
cryosparc_P44_J157_008_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
-0.18736930 0.36906386 -0.91032116 293.32936495
-0.45197081 0.79041567 0.41347969 42.75386564
0.87213252 0.48891199 0.01870646 -63.85724868
Axis 0.03840931 -0.90760614 -0.41806197
Axis point 176.77928159 0.00000000 91.68123474
Rotation angle (degrees) 100.90164196
Shift along axis -0.84080456
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.20232,-0.047684,0.97816,-32.539,-0.9291,0.30639,0.20711,241.32,-0.30958,-0.95071,0.017686,379.38
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.20232,-0.047684,0.97816,-34.112,-0.9291,0.30639,0.20711,227.45,-0.30958,-0.95071,0.017686,363.46
> fitmap #4 inMap #2
Fit map cryosparc_P44_J146_class_03_02800_volume.mrc in map
cryosparc_P44_J157_008_volume_map.mrc using 20964 points
correlation = 0.8612, correlation about mean = 0.5843, overlap = 5074
steps = 236, shift = 21.3, angle = 4.82 degrees
Position of cryosparc_P44_J146_class_03_02800_volume.mrc (#4) relative to
cryosparc_P44_J157_008_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.20149465 -0.05672380 0.97784575 -12.13204105
-0.95145154 0.22581851 0.20915536 249.97131407
-0.23267975 -0.97251653 -0.00846872 361.07684783
Axis -0.61747933 0.63255671 -0.46753747
Axis point 326.66968297 0.00000000 281.18783535
Rotation angle (degrees) 106.89255028
Shift along axis -3.20464176
> select subtract #4
Nothing selected
> hide #!1 models
> hide #!2 models
> show #!3 models
> volume #3 level 0.6257
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> volume #3 level 0.2385
> color #3 #b2ffffff models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P44_J158_005_volume_map.mrc
Opened cryosparc_P44_J158_005_volume_map.mrc as #5, grid size 512,512,512,
pixel 0.664, shown at level 0.0785, step 2, values float32
> hide #!3 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P44_J146_class_04_final_volume.mrc
Opened cryosparc_P44_J146_class_04_final_volume.mrc as #6, grid size
128,128,128, pixel 2.66, shown at level 1.09, step 1, values float32
> select add #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.81979,0.080348,0.567,204.43,-0.49015,0.41353,-0.76729,319.1,-0.29612,-0.90694,-0.29963,432.73
> select subtract #6
Nothing selected
> hide #!6 models
> volume #5 level 0.04096
> show #!6 models
> hide #!5 models
> show #!5 models
> ui tool show "Fit in Map"
> fitmap #5 inMap #6
Fit map cryosparc_P44_J158_005_volume_map.mrc in map
cryosparc_P44_J146_class_04_final_volume.mrc using 254141 points
correlation = 0.866, correlation about mean = 0.439, overlap = 3.465e+04
steps = 152, shift = 16.8, angle = 32.6 degrees
Position of cryosparc_P44_J158_005_volume_map.mrc (#5) relative to
cryosparc_P44_J146_class_04_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
-0.69376236 -0.62549279 -0.35700502 456.67325866
-0.28990982 0.69630602 -0.65658985 215.00216326
0.65927695 -0.35201806 -0.66440740 219.16033358
Axis 0.27371129 -0.91330798 0.30158028
Axis point 223.82996117 0.00000000 221.28971515
Rotation angle (degrees) 146.19458236
Shift along axis -5.27213266
> color #5 #ffb2b284 models
> color #5 #ffb2b285 models
> select add #6
2 models selected
> view matrix models
> #6,-0.66289,-0.40584,0.62919,250.06,-0.41041,-0.5059,-0.7587,462.02,0.62622,-0.76116,0.1688,166.1
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.66289,-0.40584,0.62919,259.7,-0.41041,-0.5059,-0.7587,486.29,0.62622,-0.76116,0.1688,168.83
> view matrix models
> #6,-0.66289,-0.40584,0.62919,261.92,-0.41041,-0.5059,-0.7587,494.23,0.62622,-0.76116,0.1688,171.89
> view matrix models
> #6,-0.66289,-0.40584,0.62919,263.4,-0.41041,-0.5059,-0.7587,497.51,0.62622,-0.76116,0.1688,164.61
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.4701,0.33238,0.81764,70.156,0.60681,0.79442,0.025934,-39.133,-0.64093,0.50834,-0.57515,295.3
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.4701,0.33238,0.81764,60.715,0.60681,0.79442,0.025934,-55.316,-0.64093,0.50834,-0.57515,303.31
> fitmap #5 inMap #6
Fit map cryosparc_P44_J158_005_volume_map.mrc in map
cryosparc_P44_J146_class_04_final_volume.mrc using 254141 points
correlation = 0.854, correlation about mean = 0.3337, overlap = 3.561e+04
steps = 196, shift = 14.5, angle = 43.3 degrees
Position of cryosparc_P44_J158_005_volume_map.mrc (#5) relative to
cryosparc_P44_J146_class_04_final_volume.mrc (#6) coordinates:
Matrix rotation and translation
-0.66116627 0.73633769 -0.14375673 182.63874373
-0.14459076 0.06295930 0.98748653 18.28836201
0.73617437 0.67367867 0.06484105 -94.59309051
Axis -0.24438879 -0.68527695 -0.68605366
Axis point 114.41397956 7.51441106 0.00000000
Rotation angle (degrees) 140.05694798
Shift along axis 7.72848205
> select subtract #6
Nothing selected
> color #5 #ffb2b2ff models
> hide #!6 models
> ui tool show "Side View"
> volume #5 level 0.0769
> hide #!5 models
> show #!6 models
> volume #6 level 1.404
> hide #!6 models
> show #!2 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P44_J157_008_volume_map_sharp.mrc
Opened cryosparc_P44_J157_008_volume_map_sharp.mrc as #7, grid size
512,512,512, pixel 0.664, shown at level 0.0576, step 2, values float32
> surface dust #2 size 6.64
> surface dust #7 size 6.64
> hide #!2 models
> volume #7 level 0.111
> volume #7 level 0.1393
> volume #7 level 0.3497
> volume #7 level 0.08588
> volume #7 level 0.07332
> hide #!7 models
> show #!1 models
> hide #!1 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P44_J162_003_volume_map.mrc
Opened cryosparc_P44_J162_003_volume_map.mrc as #8, grid size 128,128,128,
pixel 2.66, shown at level 2.25, step 1, values float32
> show #!1 models
> ui tool show "Fit in Map"
> fitmap #8 inMap #1
Fit map cryosparc_P44_J162_003_volume_map.mrc in map
cryosparc_P44_J146_class_03_02800_volume.mrc using 20957 points
correlation = 0.9653, correlation about mean = 0.7696, overlap = 1.339e+05
steps = 144, shift = 19.4, angle = 31.9 degrees
Position of cryosparc_P44_J162_003_volume_map.mrc (#8) relative to
cryosparc_P44_J146_class_03_02800_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.05438513 -0.73193663 -0.67919882 420.98817292
-0.09713924 0.68085735 -0.72594576 196.68664150
0.99378380 0.02649620 -0.10812828 14.68403636
Axis 0.38762978 -0.86185767 0.32702372
Axis point 247.83517948 0.00000000 235.96344097
Rotation angle (degrees) 103.93541630
Shift along axis -1.52631092
> hide #!1 models
> show #!2 models
> hide #!2 models
===== Log before crash end =====
Log:
Startup Messages
---
warning | Registration file '/Users/joanapaulino/Library/Application Support/ChimeraX/registration' has expired
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/joanapaulino/Documents/UConnHealth/Projects/Pirate_Project/fold_denguebrillrun3/fold_denguebrillrun3_model_0.cif
Chain information for fold_denguebrillrun3_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/joanapaulino/Documents/UConnHealth/Projects/Pirate_Project/fold_denguebrillrun3/fold_denguebrillrun3_model_1.cif
Chain information for fold_denguebrillrun3_model_1.cif #2
---
Chain | Description
A | .
> open
> /Users/joanapaulino/Documents/UConnHealth/Projects/Pirate_Project/fold_denguebrillrun3/fold_denguebrillrun3_model_2.cif
Chain information for fold_denguebrillrun3_model_2.cif #3
---
Chain | Description
A | .
> open
> /Users/joanapaulino/Documents/UConnHealth/Projects/Pirate_Project/fold_denguebrillrun3/fold_denguebrillrun3_model_3.cif
Chain information for fold_denguebrillrun3_model_3.cif #4
---
Chain | Description
A | .
> open
> /Users/joanapaulino/Documents/UConnHealth/Projects/Pirate_Project/fold_denguebrillrun3/fold_denguebrillrun3_model_4.cif
Chain information for fold_denguebrillrun3_model_4.cif #5
---
Chain | Description
A | .
> ui tool show Registration
Computing secondary structure
[Repeated 3 time(s)]
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0)
OS Loader Version: 577.140.2~30
Software:
System Software Overview:
System Version: macOS 13.7.6 (22H625)
Kernel Version: Darwin 22.6.0
Time since boot: 1 hour, 15 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
DELL P3424WE:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 4P2B6T3
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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