![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 weeks ago
Closed 8 weeks ago
#18632 closed defect (duplicate)
mshMIGPerform crash in NSAccessiblity native Mac APIs
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000038bed3000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001fdb260c0 (most recent call first):
File "/Applications/ChimeraX.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.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.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.surface._surface, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 59)
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{
"uptime" : 240000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "Mac16,8",
"coalitionID" : 7189,
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"build" : "24G84",
"releaseType" : "User"
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"captureTime" : "2025-08-26 19:04:52.2688 -0500",
"codeSigningMonitor" : 2,
"incident" : "09E85484-4211-4E2F-98C2-3435961CFA2A",
"pid" : 43340,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-26 18:50:10.7705 -0500",
"procStartAbsTime" : 5772379562449,
"procExitAbsTime" : 5793536362558,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5ECB94E4-9AAB-5888-B3C2-BE6A5A7F434C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "73B6F41C-450E-8CF9-DF9C-04844137B89B",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "176E7955-D0B0-4882-AE71-71FB6EB9F092",
"wakeTime" : 2038,
"sleepWakeUUID" : "FE1DA373-6C33-4A51-A928-781AD88378CB",
"sip" : "enabled",
"vmRegionInfo" : "0x1e is not in any region. Bytes before following region: 4340449250\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102b60000-102b64000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000000001e","rawCodes":[1,30],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000001e"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":43340},
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/250826.cxs
Opened cryosparc_P5_J157_008_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.968, shown at level 0.194, step 1, values float32
Opened emd_31442 (1) copy.map as #2, grid size 272,272,272, pixel 0.86, shown
at level 0.38, step 2, values float32
Log from Tue Aug 26 15:42:57 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/cryosparc_P5_J157_008_volume_map_sharp.mrc
Opened cryosparc_P5_J157_008_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.968, shown at level 0.0922, step 1, values float32
> volume #1 level 0.1939
> surface dust #1 size 9.68
> open "/Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/emd_31442 (1)
> copy.map"
Opened emd_31442 (1) copy.map as #2, grid size 272,272,272, pixel 0.86, shown
at level 0.201, step 2, values float32
> open /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/7f3x.pdb
7f3x.pdb title:
Lysophospholipid acyltransferase LPCAT3 In complex with
lysophosphatidylcholine [more info...]
Chain information for 7f3x.pdb #3
---
Chain | Description
A B | LPCAT3
Non-standard residues in 7f3x.pdb #3
---
LAP — [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-
oxy)-ethyl]-trimethylammonium (L-ALFA-lysophosphatidylcholine, lauroyl)
> open
> /Users/s230038/Projects_JieL/mboat1:2/Structure/Prediction/M2/AF-Q6ZWT7-F1-model_v4.pdb
AF-Q6ZWT7-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for lysophospholipid acyltransferase 2
(Q6ZWT7) [more info...]
Chain information for AF-Q6ZWT7-F1-model_v4.pdb #4
---
Chain | Description | UniProt
A | lysophospholipid acyltransferase 2 | MBOA2_HUMAN 1-520
> open
> /Users/s230038/Projects_JieL/mboat1:2/Structure/Prediction/M2/AF-Q6ZWT7-F1-model_v4.pdb
AF-Q6ZWT7-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for lysophospholipid acyltransferase 2
(Q6ZWT7) [more info...]
Chain information for AF-Q6ZWT7-F1-model_v4.pdb #5
---
Chain | Description | UniProt
A | lysophospholipid acyltransferase 2 | MBOA2_HUMAN 1-520
> volume #2 level 0.3799
> vop zflip # 1
> volume zflip # 1
Expected a density maps specifier or a keyword
> volume #1 flipNormals z
Invalid "flipNormals" argument: Expected true or false (or 1 or 0)
> turn z 180 models #1
> ui mousemode right "translate selected models"
> select add #1
2 models selected
> view matrix models
> #1,-0.6818,-0.3553,0.63947,131.33,-0.3553,-0.60329,-0.71401,302.7,0.63947,-0.71401,0.28509,115.7
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.36783,-0.67338,0.64129,40.467,-0.82616,0.079882,0.55774,115.73,-0.4268,-0.73496,-0.52694,353
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.36783,-0.67338,0.64129,58.135,-0.82616,0.079882,0.55774,141.15,-0.4268,-0.73496,-0.52694,331.91
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.29555,-0.87473,0.38405,197.77,-0.93605,0.34551,0.066612,183.9,-0.19096,-0.3398,-0.92091,303.5
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.29555,-0.87473,0.38405,176.93,-0.93605,0.34551,0.066612,149.88,-0.19096,-0.3398,-0.92091,255.4
> volume #2 color #ffffb252
> view matrix models
> #1,-0.29555,-0.87473,0.38405,182.02,-0.93605,0.34551,0.066612,125.72,-0.19096,-0.3398,-0.92091,240.07
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.29555,-0.87473,0.38405,212.25,-0.93605,0.34551,0.066612,187.14,-0.19096,-0.3398,-0.92091,286.3
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.38122,-0.87231,0.30618,232.4,-0.9071,0.41686,0.058243,175.77,-0.17844,-0.25553,-0.95019,278.01
> view matrix models
> #1,-0.66657,-0.72243,-0.18379,311.09,-0.68219,0.69057,-0.24026,151.7,0.30049,-0.034774,-0.95315,191.69
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.66657,-0.72243,-0.18379,301.75,-0.68219,0.69057,-0.24026,146.21,0.30049,-0.034774,-0.95315,196.64
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1)
copy.map using 35907 points
correlation = 0.3988, correlation about mean = 0.02134, overlap = 1727
steps = 100, shift = 3.29, angle = 2.32 degrees
Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to
emd_31442 (1) copy.map (#2) coordinates:
Matrix rotation and translation
-0.68712657 -0.69650141 -0.20674354 304.49818345
-0.65813608 0.71724043 -0.22896086 135.33178890
0.30775642 -0.02125974 -0.95122764 193.06643960
Axis 0.37345092 -0.92508159 0.06898166
Axis point 164.77416164 0.00000000 124.87000349
Rotation angle (degrees) 163.85414125
Shift along axis 1.84022591
> view matrix models
> #1,-0.68713,-0.6965,-0.20674,305.73,-0.65814,0.71724,-0.22896,136.66,0.30776,-0.02126,-0.95123,192.88
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.67249,-0.57949,-0.46038,321.47,-0.71598,0.66691,0.20639,95.065,0.18743,0.46842,-0.8634,136.02
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.67249,-0.57949,-0.46038,317.24,-0.71598,0.66691,0.20639,99.239,0.18743,0.46842,-0.8634,136.68
> fitmap #1 inMap #2
Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1)
copy.map using 35907 points
correlation = 0.4155, correlation about mean = 0.04248, overlap = 1789
steps = 100, shift = 2.12, angle = 11.6 degrees
Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to
emd_31442 (1) copy.map (#2) coordinates:
Matrix rotation and translation
-0.70239863 -0.64990492 -0.29027533 308.10200003
-0.70241308 0.69884856 0.13500587 103.97346773
0.11511755 0.29872110 -0.94737196 175.64973182
Axis 0.37178907 -0.92062691 -0.11924339
Axis point 164.42846237 0.00000000 99.78879984
Rotation angle (degrees) 167.28085305
Shift along axis -2.11688376
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.65447,-0.71606,-0.24275,304.36,-0.75439,0.6399,0.14636,116.28,0.050531,0.27892,-0.95898,187.57
> view matrix models
> #1,-0.52355,-0.82963,-0.19394,296.04,-0.84821,0.48609,0.21037,138.88,-0.080254,0.27465,-0.95819,204.21
> fitmap #1 inMap #2
Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1)
copy.map using 35907 points
correlation = 0.4072, correlation about mean = 0.07536, overlap = 1800
steps = 284, shift = 6.44, angle = 10.8 degrees
Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to
emd_31442 (1) copy.map (#2) coordinates:
Matrix rotation and translation
-0.41639192 -0.90486798 -0.08849704 283.42770145
-0.90679873 0.40627898 0.11248769 165.43159725
-0.06583199 0.12708793 -0.98970439 221.42313198
Axis 0.54015765 -0.83852688 -0.07143096
Axis point 194.10544743 0.00000000 104.81052587
Rotation angle (degrees) 179.22563553
Shift along axis -1.43966854
> hide #4 models
> hide #5 models
> save /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/250826.cxs
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #3 models
> show #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.62852,-0.76641,-0.1326,298.13,-0.77614,0.6069,0.1711,116.98,-0.050658,0.21045,-0.97629,207.52
> view matrix models
> #1,-0.64368,0.50169,-0.57792,199.15,0.23414,-0.58985,-0.77283,259.33,-0.7286,-0.63276,0.26221,239.53
> view matrix models
> #1,-0.45788,0.78674,-0.41399,120.1,0.84628,0.52836,0.068102,-61.294,0.27232,-0.31917,-0.90773,224.46
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.45788,0.78674,-0.41399,137.47,0.84628,0.52836,0.068102,-51.497,0.27232,-0.31917,-0.90773,225.94
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.37089,0.37043,-0.8516,233.55,0.77388,-0.38363,-0.50392,142.73,-0.51337,-0.84594,-0.14439,292.12
> view matrix models
> #1,-0.75504,0.48144,-0.44512,216.04,0.4895,-0.037777,-0.87118,181.52,-0.43624,-0.87566,-0.20714,294.17
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.75504,0.48144,-0.44512,212.61,0.4895,-0.037777,-0.87118,176.02,-0.43624,-0.87566,-0.20714,303.94
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.29164,0.64518,-0.70618,167.89,0.9306,0.36212,-0.053478,-31.484,0.22122,-0.67277,-0.70601,260.37
> view matrix models
> #1,-0.29894,0.4985,-0.81372,200.55,0.7869,-0.35361,-0.50571,132.13,-0.53983,-0.79149,-0.28657,316.38
> view matrix models
> #1,0.57958,0.65328,-0.48714,31.265,-0.73956,0.17061,-0.6511,274.68,-0.34224,0.73764,0.58203,-7.2889
> view matrix models
> #1,0.56591,0.61347,-0.55082,45.938,-0.75915,0.12709,-0.63839,280.89,-0.32163,0.77943,0.53763,-9.4118
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.56591,0.61347,-0.55082,25.765,-0.75915,0.12709,-0.63839,296.07,-0.32163,0.77943,0.53763,-5.6319
> fitmap #1 inMap #2
Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1)
copy.map using 35907 points
correlation = 0.4291, correlation about mean = 0.05808, overlap = 1413
steps = 80, shift = 1.66, angle = 3.98 degrees
Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to
emd_31442 (1) copy.map (#2) coordinates:
Matrix rotation and translation
0.60314778 0.61485029 -0.50810619 17.09187444
-0.73936907 0.19198720 -0.64534817 286.90572149
-0.29924264 0.76491833 0.57039796 -10.25848893
Axis 0.71721375 -0.10622092 -0.68871007
Axis point 0.00000000 159.76350051 242.70653410
Rotation angle (degrees) 79.46905946
Shift along axis -11.15173722
> view matrix models
> #1,0.60315,0.61485,-0.50811,19.64,-0.73937,0.19199,-0.64535,279.66,-0.29924,0.76492,0.5704,-15.967
> view matrix models
> #1,0.60315,0.61485,-0.50811,12.419,-0.73937,0.19199,-0.64535,291.15,-0.29924,0.76492,0.5704,-9.9911
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.60315,0.61485,-0.50811,31.422,-0.73937,0.19199,-0.64535,255.82,-0.29924,0.76492,0.5704,-16.34
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.020597,0.24228,-0.96999,208.11,-0.7924,0.59557,0.13193,114.19,0.60966,0.7659,0.20425,-82.817
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.020597,0.24228,-0.96999,207.5,-0.7924,0.59557,0.13193,123.43,0.60966,0.7659,0.20425,-85.938
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.25815,0.13535,-0.95658,253.59,-0.28409,0.93573,0.20907,8.5555,0.92339,0.32573,-0.2031,-18.81
> view matrix models
> #1,0.12323,-0.33895,-0.9327,262.08,-0.16763,0.91925,-0.35621,67.581,0.97812,0.20024,0.056458,-42.833
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.12323,-0.33895,-0.9327,256.39,-0.16763,0.91925,-0.35621,70.038,0.97812,0.20024,0.056458,-52.348
> view matrix models
> #1,0.12323,-0.33895,-0.9327,237.51,-0.16763,0.91925,-0.35621,148.44,0.97812,0.20024,0.056458,-78.819
> view matrix models
> #1,0.12323,-0.33895,-0.9327,232.4,-0.16763,0.91925,-0.35621,167.19,0.97812,0.20024,0.056458,-76.469
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.82535,-0.55581,0.099368,246.41,-0.55358,0.76196,-0.33611,231.96,0.1111,-0.33242,-0.93657,222.4
> volume #1 color #b2b2b29f
> set bgColor white
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.91681,-0.38005,0.12257,233.04,-0.39382,0.80969,-0.4351,218.76,0.066111,-0.44717,-0.892,236.56
> view matrix models
> #1,-0.94422,0.32386,0.059735,157.16,0.28889,0.72747,0.62236,10.764,0.1581,0.6049,-0.78045,80.724
> view matrix models
> #1,-0.54076,0.81634,-0.20289,79.33,0.55171,0.52628,0.64703,0.011378,0.63497,0.23795,-0.73498,61.359
> view matrix models
> #1,0.40711,0.58493,0.70151,-123.7,0.91239,-0.22472,-0.34211,173.33,-0.042468,0.77933,-0.62517,64.345
> view matrix models
> #1,0.4719,0.88113,0.030238,-83.619,0.75438,-0.3858,-0.5311,236.74,-0.4563,0.27344,-0.84677,206.29
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.4719,0.88113,0.030238,-40.179,0.75438,-0.3858,-0.5311,135.64,-0.4563,0.27344,-0.84677,241.96
> view matrix models
> #1,0.4719,0.88113,0.030238,-46.784,0.75438,-0.3858,-0.5311,138.31,-0.4563,0.27344,-0.84677,241.06
> fitmap #1 inMap #2
Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1)
copy.map using 35907 points
correlation = 0.4112, correlation about mean = 0.05985, overlap = 1821
steps = 112, shift = 2.99, angle = 11.8 degrees
Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to
emd_31442 (1) copy.map (#2) coordinates:
Matrix rotation and translation
0.45951627 0.88101964 0.11246871 -56.63973154
0.84526238 -0.39491411 -0.35996445 104.14962316
-0.27272024 0.26047506 -0.92616218 231.47216333
Axis 0.84856924 0.52681928 -0.04890487
Axis point -0.00000000 43.85689839 125.98886915
Rotation angle (degrees) 158.55673239
Shift along axis -4.51482007
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.42804,0.90371,-0.0095249,-40.139,0.9034,-0.42755,0.032658,51.388,0.025441,-0.022584,-0.99942,238.86
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.42804,0.90371,-0.0095249,-36.614,0.9034,-0.42755,0.032658,47.54,0.025441,-0.022584,-0.99942,237.93
> view matrix models
> #1,0.42804,0.90371,-0.0095249,-33.097,0.9034,-0.42755,0.032658,43.517,0.025441,-0.022584,-0.99942,240.7
> view matrix models
> #1,0.42804,0.90371,-0.0095249,-31.397,0.9034,-0.42755,0.032658,42.985,0.025441,-0.022584,-0.99942,240.62
> view matrix models
> #1,0.42804,0.90371,-0.0095249,-34.097,0.9034,-0.42755,0.032658,44.633,0.025441,-0.022584,-0.99942,239.94
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.47868,0.87783,0.016754,-40.485,0.85481,-0.4616,-0.23713,88.957,-0.20043,0.12783,-0.97133,245.74
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.47868,0.87783,0.016754,-43.136,0.85481,-0.4616,-0.23713,94.909,-0.20043,0.12783,-0.97133,240.71
> fitmap #1 inMap #2
Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1)
copy.map using 35907 points
correlation = 0.4149, correlation about mean = 0.05652, overlap = 1773
steps = 136, shift = 3.68, angle = 9.25 degrees
Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to
emd_31442 (1) copy.map (#2) coordinates:
Matrix rotation and translation
0.58959800 0.80561011 0.05802220 -49.50542004
0.80195294 -0.57534064 -0.16079383 106.05933050
-0.09615458 0.14133476 -0.98528106 227.44902909
Axis 0.89067485 0.45451301 -0.01078132
Axis point 0.00000000 54.75316690 118.47463635
Rotation angle (degrees) 170.23505584
Shift along axis 1.65991125
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.5896,0.80561,0.058022,-19.604,0.80195,-0.57534,-0.16079,209.01,-0.096155,0.14133,-0.98528,254.46
> view matrix models
> #1,0.5896,0.80561,0.058022,-55.156,0.80195,-0.57534,-0.16079,245.22,-0.096155,0.14133,-0.98528,266.81
> show #4 models
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 4199 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 4199, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.58959799 0.80195292 -0.09615460 -138.48411228
0.80561009 -0.57534063 0.14133479 147.81220800
0.05802219 -0.16079379 -0.98528107 305.51472320
Axis -0.89067482 -0.45451307 0.01078134
Axis point 0.00000000 123.86024254 143.53521853
Rotation angle (degrees) 170.23505596
Shift along axis 59.45558924
> select subtract #1
Nothing selected
> select add #4
4199 atoms, 4309 bonds, 520 residues, 1 model selected
> view matrix models #4,1,0,0,34.907,0,1,0,293.13,0,0,1,-16.131
> view matrix models #4,1,0,0,148.49,0,1,0,239.83,0,0,1,30.839
> view matrix models #4,1,0,0,149.36,0,1,0,239.33,0,0,1,29.272
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.32401,-0.3039,-0.89591,147.14,0.6647,0.60074,-0.44417,235.4,0.67319,-0.73943,0.007356,22.221
> view matrix models
> #4,0.68619,0.41396,0.59814,153.3,0.074378,0.77805,-0.62379,237.02,-0.72361,0.47253,0.5031,33.005
> view matrix models
> #4,0.43981,0.89193,0.10501,156.75,0.044019,0.095373,-0.99447,231.43,-0.89701,0.442,0.0026844,32.457
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.43981,0.89193,0.10501,117.1,0.044019,0.095373,-0.99447,317.83,-0.89701,0.442,0.0026844,121.05
> select clear
> select #4/A:480
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
126 atoms, 127 bonds, 15 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/A:488
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
21 atoms, 20 bonds, 3 residues, 1 model selected
> select up
261 atoms, 262 bonds, 34 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/A:466
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
78 atoms, 78 bonds, 9 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui mousemode right "rotate selected models"
> select add #4
3734 atoms, 3839 bonds, 462 residues, 1 model selected
> view matrix models
> #4,0.43405,0.89787,0.07366,117.05,-0.36089,0.24821,-0.89897,316.05,-0.82544,0.36362,0.43177,121.76
> view matrix models
> #4,-0.55307,0.07934,-0.82935,108.63,-0.81339,-0.26687,0.51689,313.99,-0.18032,0.96046,0.21213,126.46
> view matrix models
> #4,-0.46087,-0.34196,-0.81894,108.18,-0.789,-0.26458,0.5545,314.17,-0.40629,0.9017,-0.14787,124.66
> view matrix models
> #4,-0.43468,-0.32294,-0.84069,108.35,-0.48585,-0.70191,0.52083,314.8,-0.75829,0.63484,0.14821,122.43
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.43468,-0.32294,-0.84069,107.43,-0.48585,-0.70191,0.52083,272.7,-0.75829,0.63484,0.14821,134.16
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.50319,-0.32511,-0.80069,107.1,-0.56202,-0.58071,0.58899,272.64,-0.65646,0.74637,0.10949,134.93
> view matrix models
> #4,-0.2983,-0.22446,-0.9277,108.32,-0.7934,-0.482,0.37174,271.33,-0.53059,0.84693,-0.034304,135.7
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.2983,-0.22446,-0.9277,110.42,-0.7934,-0.482,0.37174,253.47,-0.53059,0.84693,-0.034304,138.15
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.40927,0.0086167,-0.91237,110.37,-0.67444,-0.67634,0.29615,253.59,-0.61452,0.73654,0.28262,137.8
> view matrix models
> #4,-0.45763,-0.047851,-0.88786,109.99,-0.65112,-0.66196,0.37128,253.84,-0.60549,0.74801,0.27177,137.87
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.45763,-0.047851,-0.88786,110.2,-0.65112,-0.66196,0.37128,271.56,-0.60549,0.74801,0.27177,136.91
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms
average map value = 0.06061, steps = 92
shifted from previous position = 2.82
rotated from previous position = 9.97 degrees
atoms outside contour = 3232, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.82226951 -0.52311174 -0.22411366 131.45972009
-0.11201597 0.53487062 -0.83747587 97.22191800
0.55796526 -0.66352661 -0.49840467 131.20998200
Axis 0.19316900 -0.86849126 0.45651797
Axis point 58.62750865 0.00000000 109.13656195
Rotation angle (degrees) 153.24018107
Shift along axis 0.85727183
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.54268,0.083972,-0.83573,133.52,-0.68469,-0.62055,0.38225,324.78,-0.48652,0.77966,0.39425,130.33
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.15664,-0.23047,-0.96039,136.53,-0.96973,-0.2203,-0.10529,323.56,-0.18731,0.94781,-0.258,131.62
> view matrix models
> #4,0.34533,0.10698,-0.93236,138.39,-0.52651,-0.80032,-0.28684,324.47,-0.77688,0.58995,-0.22005,127.57
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.34533,0.10698,-0.93236,139.1,-0.52651,-0.80032,-0.28684,274.22,-0.77688,0.58995,-0.22005,151.68
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.34533,0.10698,-0.93236,119.89,-0.52651,-0.80032,-0.28684,254.68,-0.77688,0.58995,-0.22005,128.96
> view matrix models
> #4,0.34533,0.10698,-0.93236,122.45,-0.52651,-0.80032,-0.28684,256.94,-0.77688,0.58995,-0.22005,134.39
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.56153,0.08835,-0.82273,123.73,-0.48948,-0.7662,-0.41636,257.08,-0.66716,0.6365,-0.387,134.91
> view matrix models
> #4,0.51187,0.026603,-0.85865,123.27,-0.55709,-0.75058,-0.35535,256.81,-0.65394,0.66024,-0.36938,135.06
> view matrix models
> #4,0.37292,0.23786,-0.89686,122.95,-0.81519,-0.37767,-0.43913,256.14,-0.44316,0.89487,0.05306,137.26
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.69314,0.50873,-0.51063,125.8,-0.71957,0.52982,-0.44891,258.76,0.042168,0.67859,0.73331,140.24
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.69314,0.50873,-0.51063,129.43,-0.71957,0.52982,-0.44891,264.17,0.042168,0.67859,0.73331,140.79
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms
average map value = 0.06347, steps = 108
shifted from previous position = 2.88
rotated from previous position = 3.61 degrees
atoms outside contour = 3159, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.12729822 0.68087217 -0.72125462 138.51587855
0.98900174 0.14234061 -0.04018332 122.05232409
0.07530409 -0.71843734 -0.69150350 131.67605304
Axis -0.62189082 -0.73036434 0.28252387
Axis point -17.36882087 0.00000000 100.13564662
Rotation angle (degrees) 146.95373972
Shift along axis -138.08279054
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.42461,0.80905,-0.40639,131.69,-0.86712,0.23429,-0.43957,263.1,-0.26042,0.53903,0.80102,138.91
> save /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/250826.cxs
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.42461,0.80905,-0.40639,158.95,-0.86712,0.23429,-0.43957,311.78,-0.26042,0.53903,0.80102,114.79
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7f3x.pdb, chain B (#3) with AF-Q6ZWT7-F1-model_v4.pdb, chain A
(#4), sequence alignment score = 713
RMSD between 201 pruned atom pairs is 1.242 angstroms; (across all 421 pairs:
5.150)
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.7367,0.49979,-0.45549,102.09,-0.27992,-0.38778,-0.87822,314.79,-0.61556,0.77449,-0.14578,104.34
> save /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/250826.cxs
——— End of log from Tue Aug 26 15:42:57 2025 ———
> view name session-start
opened ChimeraX session
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7f3x.pdb, chain B (#3) with AF-Q6ZWT7-F1-model_v4.pdb, chain A
(#4), sequence alignment score = 713
RMSD between 201 pruned atom pairs is 1.242 angstroms; (across all 421 pairs:
5.150)
> hide #3 models
> show #3 models
> hide #!2 models
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.7367,0.49979,-0.45549,126.26,-0.27992,-0.38778,-0.87822,270.01,-0.61556,0.77449,-0.14578,133.59
> ui tool show "Fit in Map"
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms
average map value = 0.06537, steps = 96
shifted from previous position = 1.17
rotated from previous position = 6.67 degrees
atoms outside contour = 3147, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.25840829 0.02482437 -0.96571677 139.19869591
0.64480116 0.73995737 0.19155817 112.75028801
0.71934456 -0.67219556 0.17520431 138.76375878
Axis -0.43351248 -0.84572152 0.31116239
Axis point -71.37574422 0.00000000 148.43980884
Rotation angle (degrees) 85.02132379
Shift along axis -112.52165385
> view matrix models
> #4,0.71355,0.57175,-0.4049,124.85,-0.27942,-0.29773,-0.91284,269.75,-0.64247,0.7645,-0.052694,133.67
> view matrix models
> #4,0.71355,0.57175,-0.4049,124.15,-0.27942,-0.29773,-0.91284,269.38,-0.64247,0.7645,-0.052694,133.16
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms
average map value = 0.06537, steps = 56
shifted from previous position = 1.75
rotated from previous position = 0.013 degrees
atoms outside contour = 3147, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.25825859 0.02475727 -0.96575854 139.19347255
0.64473164 0.74006336 0.19138265 112.74694351
0.71946063 -0.67208134 0.17516589 138.76394098
Axis -0.43336551 -0.84579770 0.31116006
Axis point -71.34696702 0.00000000 148.44155812
Rotation angle (degrees) 85.02368525
Shift along axis -112.50495910
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.57621,0.6438,-0.50349,125.09,-0.24825,-0.44907,-0.85832,269.56,-0.77869,0.61956,-0.098932,131.5
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.57621,0.6438,-0.50349,131.02,-0.24825,-0.44907,-0.85832,271.8,-0.77869,0.61956,-0.098932,132.33
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.17359,0.7035,-0.68917,128.71,-0.43433,-0.57337,-0.6947,270.67,-0.88387,0.41992,0.20602,131.64
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.17359,0.7035,-0.68917,119.72,-0.43433,-0.57337,-0.6947,271.86,-0.88387,0.41992,0.20602,136.87
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms
average map value = 0.07018, steps = 120
shifted from previous position = 5.03
rotated from previous position = 16 degrees
atoms outside contour = 3046, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.10374815 0.04153714 -0.99373586 138.02925909
0.50330022 0.86395534 -0.01643317 111.55685728
0.85786082 -0.50185243 -0.11053945 129.71772261
Axis -0.24652112 -0.94033700 0.23450729
Axis point -14.72943306 -0.00000000 128.34117281
Rotation angle (degrees) 100.08832600
Shift along axis -108.50841656
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.42814,0.67696,-0.59869,123.79,-0.506,-0.36932,-0.77947,270.92,-0.74877,0.63666,0.18441,141.62
> view matrix models
> #4,-0.79961,-0.063497,0.59715,116.65,0.11648,0.95911,0.25796,278.65,-0.58911,0.27583,-0.75952,140.57
> view matrix models
> #4,-0.55677,0.52094,0.64701,119.41,0.82855,0.29274,0.47729,281.31,0.059235,0.80183,-0.59461,145.58
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms
average map value = 0.06685, steps = 76
shifted from previous position = 5.91
rotated from previous position = 4.3 degrees
atoms outside contour = 3207, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.32235255 0.42335464 0.84667565 143.17677766
-0.90068388 0.41240875 0.13670239 96.82990632
-0.29130282 -0.80665350 0.51424975 122.67574433
Axis -0.47537690 0.57345132 -0.66721090
Axis point 156.09290881 17.64062945 -0.00000000
Rotation angle (degrees) 82.84779842
Shift along axis -94.38628917
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.55244,0.53505,0.63916,126.35,0.82355,0.23194,0.51766,278.24,0.12872,0.81236,-0.56877,144.45
> view matrix models
> #4,-0.55244,0.53505,0.63916,113.27,0.82355,0.23194,0.51766,273.27,0.12872,0.81236,-0.56877,144.01
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.81715,0.10823,0.56617,110.73,0.56349,-0.056841,0.82416,271.52,0.12138,0.9925,-0.014541,145.03
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.81715,0.10823,0.56617,114.75,0.56349,-0.056841,0.82416,275.24,0.12138,0.9925,-0.014541,144.27
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms
average map value = 0.06383, steps = 84
shifted from previous position = 5.5
rotated from previous position = 4.89 degrees
atoms outside contour = 3140, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.04830002 -0.02580030 0.99849959 136.11761176
-0.97984546 0.19521535 -0.04235349 97.97943271
-0.19382968 -0.98042100 -0.03470919 122.74761427
Axis -0.52342970 0.66530453 -0.53234503
Axis point 146.12202994 0.00000000 54.51989508
Rotation angle (degrees) 116.35278694
Shift along axis -71.40592354
> hide #!1 models
> select clear
> select #4/A:461
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
91 atoms, 91 bonds, 12 residues, 1 model selected
> color sel red
> show #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.98374,0.17786,-0.025004,109.84,0.031442,0.3076,0.951,276.16,0.17684,0.93475,-0.30819,146.87
> view matrix models
> #4,-0.76733,-0.40179,-0.49977,109.15,-0.28152,-0.48918,0.8255,272.44,-0.57615,0.77413,0.26225,142.99
> view matrix models
> #4,0.37221,0.20811,-0.90452,116.41,-0.92518,0.0053,-0.37949,268.62,-0.074181,0.97809,0.19451,146.16
> view matrix models
> #4,0.23616,-0.094695,-0.96709,114.88,-0.69798,-0.70896,-0.10103,268.55,-0.67606,0.69886,-0.23352,141.68
> view matrix models
> #4,0.34209,0.39535,-0.85245,116.74,-0.92915,0.0069926,-0.36963,268.61,-0.14017,0.9185,0.36973,145.86
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms
average map value = 0.06762, steps = 108
shifted from previous position = 1.65
rotated from previous position = 11.8 degrees
atoms outside contour = 3121, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.54642107 -0.05423592 -0.83575262 131.60633888
0.73015310 0.45796015 -0.50709854 105.94785777
0.41024432 -0.88731674 -0.21063856 125.52547356
Axis -0.25003858 -0.81939082 0.51582885
Axis point 6.35752857 -0.00000000 129.26118427
Rotation angle (degrees) 130.50766368
Shift along axis -54.96970332
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.40792,0.47102,-0.78214,116.31,-0.79501,-0.23799,-0.55796,269.93,-0.44896,0.84941,0.27739,144.19
> view matrix models
> #4,0.78425,0.42754,-0.44963,118.68,-0.43249,-0.14291,-0.89024,271.77,-0.44487,0.89263,0.072829,144.08
> view matrix models
> #4,0.94021,0.31453,-0.13066,119.66,-0.20585,0.21913,-0.95373,273.79,-0.27135,0.92361,0.27078,145.34
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms
average map value = 0.07051, steps = 72
shifted from previous position = 2.88
rotated from previous position = 6.67 degrees
atoms outside contour = 3125, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.39787946 0.31561160 -0.86144137 138.45669809
0.87267658 0.15951182 0.46151007 108.37622873
0.28306800 -0.93538511 -0.21196042 127.22430024
Axis -0.73915600 -0.60560805 0.29476652
Axis point 0.00000000 77.25734416 77.08011521
Rotation angle (degrees) 109.10404291
Shift along axis -130.47315170
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.95405,0.26032,-0.14841,121.82,-0.22852,0.31174,-0.92228,276.13,-0.19382,0.91381,0.3569,141.92
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.66312,0.74851,-0.0019277,121.5,-0.0043303,0.001261,-0.99999,276.57,-0.7485,0.66312,0.0040775,137.86
> view matrix models
> #4,0.33713,0.50715,-0.79318,118.22,-0.85599,0.51588,-0.033978,274.16,0.39195,0.69041,0.60804,144.95
> view matrix models
> #4,-0.27304,0.25381,-0.92792,114.09,-0.9536,-0.19863,0.22627,272.26,-0.12688,0.94664,0.29626,142.3
> view matrix models
> #4,0.26572,-0.045243,-0.96299,116.35,-0.90554,-0.35442,-0.23322,271.64,-0.33075,0.93399,-0.13514,140.64
> view matrix models
> #4,0.14437,0.32743,-0.93378,116.57,-0.42674,-0.8308,-0.35729,273.05,-0.89278,0.45006,0.019787,136.58
> fitmap #4 inMap #1
Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms
average map value = 0.06965, steps = 68
shifted from previous position = 4.14
rotated from previous position = 7.07 degrees
atoms outside contour = 3054, contour level = 0.19392
Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to
cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.20600772 -0.60214270 -0.77135269 138.28257777
0.25753747 0.72710890 -0.63638596 107.29525118
0.94405257 -0.32975269 0.00528426 132.78459885
Axis 0.15780515 -0.88281280 0.44242411
Axis point 16.86859417 0.00000000 155.79423963
Rotation angle (degrees) 103.69818008
Shift along axis -14.15281015
> save /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/250826.cxs
> hide #!4 models
> show #5 models
> ui mousemode right "translate selected models"
> select add #5
4290 atoms, 4400 bonds, 532 residues, 2 models selected
> select add #4
7933 atoms, 8148 bonds, 982 residues, 2 models selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Mac16,8
Model Number: MX2F3LL/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 3 days, 19 hours, 47 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
ED343CUR V:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 100.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
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: 14.1.19
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: 1.10.1
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: 1.1.3
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: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
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: 4.3.2
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
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: 4.14.1
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
Change History (2)
comment:1 by , 8 weeks ago
| Component: | Unassigned → Platform |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → mshMIGPerform crash in NSAccessiblity native Mac APIs |
comment:2 by , 8 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #18238