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Opened 4 hours ago
#20111 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-26.3.1-arm64-arm-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 0x00000001fcfaf100 (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, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 59)
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"procRole" : "Foreground",
"version" : 2,
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"coalitionID" : 29328,
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"build" : "25D771280a",
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"captureTime" : "2026-04-02 10:19:08.0608 +0200",
"codeSigningMonitor" : 1,
"incident" : "C3E4D8D4-1CC9-4757-8C63-130EFAF1AC3E",
"pid" : 36038,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-03-31 23:06:13.7460 +0200",
"procStartAbsTime" : 2848103281773,
"procExitAbsTime" : 4561386521771,
"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":"D91302BD-DBCE-5C53-8136-7D7F3BF49D6F","thirdParty":true},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F0D674B1-5FA4-E9D0-6B9C-8D1ED9987542",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "DE24FC23-137F-4374-BBCF-2972FC095D6A",
"wakeTime" : 9,
"sleepWakeUUID" : "382AD593-C110-4DE9-B578-71F304D8D343",
"sip" : "enabled",
"vmRegionInfo" : "0x171 is not in any region. Bytes before following region: 4372545167\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1049fc000-104a00000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000171","rawCodes":[1,369],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000171"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":36038},
"vmregioninfo" : "0x171 is not in any region. Bytes before following region: 4372545167\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1049fc000-104a00000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
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"vmSummary" : "ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%)\nWritable regions: Total=3.5G written=21.2M(1%) resident=2747K(0%) swapped_out=18.6M(1%) unallocated=3.5G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \n.note.gnu.proper 320 1 \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nAttributeGraph Data 1024K 1 \nCG image 720K 21 \nColorSync 144K 9 \nCoreAnimation 4592K 212 \nCoreGraphics 80K 5 \nCoreServices 624K 2 \nCoreUI image data 5392K 40 \nFoundation 48K 2 \nKernel Alloc Once 48K 2 \nMALLOC 2.8G 738 \nMALLOC guard page 3792K 4 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 624K 39 \nStack 200.8M 40 \nStack Guard 56.0M 1 \nVM_ALLOCATE 365.4M 369 \nVM_ALLOCATE (reserved) 192.0M 1 reserved VM address space (unallocated)\n__AUTH 5968K 656 \n__AUTH_CONST 90.5M 1042 \n__CTF 824 1 \n__DATA 46.7M 1154 \n__DATA_CONST 43.4M 1200 \n__DATA_DIRTY 8499K 899 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5176K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 619.0M 154 \n__OBJC_RO 78.4M 1 \n__OBJC_RW 2571K 1 \n__TEXT 1.5G 1179 \n__TEXT (graphics) 7088K 43 \n__TPRO_CONST 128K 2 \ndyld private memory 3120K 26 \nmapped file 672.0M 109 \npage table in kernel 2747K 1 \nshared memory 4384K 38 \n=========== ======= ======= \nTOTAL 6.6G 8004 \nTOTAL, minus reserved VM space 6.4G 8004 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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},
"logWritingSignature" : "f62354508c8ceb402b3ebc9740251316759060eb",
"bug_type" : "309",
"roots_installed" : 0,
"trmStatus" : 1,
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "644114de41e7236e6177f9bd",
"factorPackIds" : [
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{
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===== Log before crash start =====
> graphics silhouettes true
> lighting soft
> windowsize 800 800
> ui tool hide "command line interface"
> ui tool show clix
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/kelvinlau/Desktop/RhGB07-full/v7/RBD zoomed in-more-
> clade1-v7.cxs" format session
Opened 103_zflipped.ccp4 as #2, grid size 300,300,300, pixel 1.38, shown at
level 0.184, step 1, values float32
Opened 103_sharp_zflipped.ccp4 as #3, grid size 300,300,300, pixel 1.38, shown
at level 0.239, step 1, values float32
Opened 103_zflipped.ccp4 1 as #6.2, grid size 300,300,300, pixel 1.38, shown
at level 0.19, step 1, values float32
> view name session-start
opened ChimeraX session
> ui tool show "Command Line Interface"
> toolshed show
> ui tool show "Command Line Interface"
> ui tool show clix
> rename #11 sarscov2closed
> rename #12 5x58
> rename #12 sarscov1 closed
Expected a keyword
> rename #12 sarscov1closed
> hide #!11 models
> hide #!12 models
> show #!10 models
> show #!9 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!10 models
> hide #!4 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> open /Users/kelvinlau/Downloads/7DF3.pdb
7DF3.pdb title:
Sars-cov-2 S trimer, S-closed [more info...]
Chain information for 7DF3.pdb #13
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2 1-1208
Non-standard residues in 7DF3.pdb #13
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> show #!4 models
> hide #!4 models
> show #!4 models
> mmaker #13 to #4
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 30B-RBD-only.pdb, chain A (#4) with 7DF3.pdb, chain A (#13),
sequence alignment score = 636.7
RMSD between 163 pruned atom pairs is 1.064 angstroms; (across all 179 pairs:
1.808)
> close #11
> rename #13 sarscov2closed
> color #12 #5272aaff
> color #13 #b44e66ff
> hide #!4 models
> hide #!13 models
> show #!9 models
> hide #!12 models
> hide #!9 models
> show #!12 models
> select #12/A:320-503
1480 atoms, 1528 bonds, 184 residues, 1 model selected
> show #!9 models
> select ~sel & ##selected
23785 atoms, 24387 bonds, 9 pseudobonds, 3017 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> hide #!9 models
> close #9
> hide sel cartoons
> show sel atoms
> hide sel atoms
> select clear
Drag select of 56 atoms, 184 residues, 50 bonds
> hide sel cartoons
> hide sel atoms
> show sel atoms
> style sel ball
Changed 1480 atom styles
> style sel sphere
Changed 1480 atom styles
> style sel ball
Changed 1480 atom styles
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
> hide #!12 models
> show #!10 models
> show #!13 models
> select #13/A:333-516
1469 atoms, 1513 bonds, 184 residues, 1 model selected
> hide #!10 models
> select ~sel & ##selected
25126 atoms, 25787 bonds, 12 pseudobonds, 3158 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select clear
Drag select of 32 atoms, 184 residues, 26 bonds
> hide sel atoms
> hide sel cartoons
> show sel atoms
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> style sel ball
Changed 1469 atom styles
> select clear
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> close #10
> show #!12 models
> show #!4 models
> save "/Users/kelvinlau/Desktop/RhGB07-full/v7/RBD zoomed in-more-
> clade1-v7.cxs"
> save /Users/kelvinlau/Desktop/image1.png supersample 3
> ui tool show "Side View"
> save /Users/kelvinlau/Desktop/image2.png supersample 3
> save /Users/kelvinlau/Desktop/image3.png supersample 3
> hide #!12 models
> hide #!13 models
> hide #!4 models
> show #!1 models
> hide #!1 atoms
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> ui tool show "Show Sequence Viewer"
FYI: command is replacing existing command: "sequence align"
FYI: command is replacing existing command: "sequence associate"
FYI: command is replacing existing command: "sequence chain"
FYI: command is replacing existing command: "sequence disassociate"
FYI: command is replacing existing command: "sequence dissociate"
FYI: command is replacing existing command: "sequence expandsel"
FYI: command is replacing existing command: "sequence header"
FYI: command is replacing existing command: "sequence identity"
FYI: command is replacing existing command: "sequence match"
FYI: command is replacing existing command: "sequence refseq"
FYI: command is replacing existing command: "sequence refreshAttrs"
FYI: command is replacing existing command: "sequence rename"
FYI: command is replacing existing command: "sequence update"
FYI: command is replacing existing command: "sequence grid"
FYI: command is replacing existing command: "sequence viewer"
> sequence chain #1/A #1/B #1/C
Alignment identifier is 1
> select #1/A-C:201
30 atoms, 30 bonds, 3 residues, 1 model selected
> select #1/A-C:201-204
117 atoms, 120 bonds, 12 residues, 1 model selected
> volume #2 color #b2b2b280
> select
> #1/A-C:32-34,51-59,65-70,92-98,103-109,118-123,127-133,135-137,144-146,149-152,156-159,184-193,196-204,220-226,233-238,255-260,262-270,276-281,302-305,345-349,368-372,387-394,423-429,440-442,479-481,496-502,526-530,535-539,563-566,571-574,583-587,598-601,632-634,638-641,654-657,660-664,675-679,695-697,700-711,716-718,842-844,1030-1039,1042-1053,1056-1058,1071-1073,1077-1080,1085-1088,1103-1105
6435 atoms, 6504 bonds, 786 residues, 1 model selected
> select #1/A-C:106
42 atoms, 45 bonds, 3 residues, 1 model selected
> select #1/A-C:106
42 atoms, 45 bonds, 3 residues, 1 model selected
> select #1/A-C:102
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #1/A-C:102
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #1/A-C:102
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #1/A-C:102,106
63 atoms, 63 bonds, 6 residues, 1 model selected
> select #1/A-C:102,106,121
87 atoms, 84 bonds, 9 residues, 1 model selected
> select #1/A-C:102,106,121,123
111 atoms, 105 bonds, 12 residues, 1 model selected
> select #1/A-C:102,106,121,123,128
135 atoms, 126 bonds, 15 residues, 1 model selected
> select #1/A-C:102,106,121,123,128,186
168 atoms, 156 bonds, 18 residues, 1 model selected
> select #1/A-C:102,106,121,123,128,186,188
198 atoms, 186 bonds, 21 residues, 1 model selected
> select #1/A-C:102,106,121,123,128,186,188,203
234 atoms, 222 bonds, 24 residues, 1 model selected
> select #1/A-C:102,106,121,123,128,186,188,203,222-223
291 atoms, 279 bonds, 30 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 291 atom styles
> color sel byhetero
> name sel bili
"sel" is reserved and cannot be redefined
> select name bili
Expected an objects specifier or a keyword
> name bili sel
> select #1/A-C:102,106,121,123,128,186,188,203,222-223
291 atoms, 279 bonds, 30 residues, 1 model selected
> select #1/A-C:102,106,121,123,128,186,188,203,222-223
291 atoms, 279 bonds, 30 residues, 1 model selected
> select #1/A-C:102-104,106,121,123,128,186,188,203,222-223
345 atoms, 333 bonds, 36 residues, 1 model selected
> select #1/A-C:102-104,106,121,123,128,186,188,203,222-223
345 atoms, 333 bonds, 36 residues, 1 model selected
> select #1/A-C:102-104,106,121,123,128,186,188,203,222-223
345 atoms, 333 bonds, 36 residues, 1 model selected
> select #1/A-C:102-104,106,121,123,128,186,188,203,222-223
345 atoms, 333 bonds, 36 residues, 1 model selected
> hide sel atoms
> select #1/A-C:103,106,121,123,128,186,188,203,222-223
291 atoms, 279 bonds, 30 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 291 atom styles
> select clear
> select #1/A-C:90
30 atoms, 30 bonds, 3 residues, 1 model selected
> select #1/A-C:90-282
4248 atoms, 4368 bonds, 3 pseudobonds, 537 residues, 2 models selected
> ui tool show "Surface Zone"
> surface zone #2 nearAtoms #1 distance 5
> surface zone #2 nearAtoms sel distance 5
> select clear
> recenter
Unknown command: recenter
> center
Unknown command: center
> show #!3 models
> hide #!3 models
> select #1/B:33
11 atoms, 11 bonds, 1 residue, 1 model selected
> cofr sel
> select clear
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> select #1/A:103
7 atoms, 6 bonds, 1 residue, 1 model selected
> cofr sel
> select clear
> volume #2 level 0.1591
> volume #2 level 0.1528
> volume #2 level 0.1864
> select #1/A-C:103,106,121,123,128,186,188,203,222-223
291 atoms, 279 bonds, 30 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #b44e66ff target a
> color sel byhetero target a
> select clear
> save /Users/kelvinlau/Desktop/image1.png supersample 3
No atoms selected for zoning
> save /Users/kelvinlau/Desktop/image2.png supersample 3
> hide #!2 models
> save /Users/kelvinlau/Desktop/RhGB07-full/v7/biliverdin.cxs
> select #1/A-C:383
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A-C:383
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A-C:383
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A-C:383,424-425
57 atoms, 51 bonds, 9 residues, 1 model selected
Drag select of 2 residues
> select #1/A-C:383
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A-C:383
18 atoms, 15 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> hide sel atoms
> select #1/A-C:371
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A-C:371
18 atoms, 15 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> hide sel atoms
> select #1/A-C:327,371
36 atoms, 30 bonds, 6 residues, 1 model selected
> select #1/A-C:327
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A-C:325-327
69 atoms, 66 bonds, 9 residues, 1 model selected
> select #1/A-C:327
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A-C:327
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A-C:327,352
36 atoms, 33 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 36 atom styles
> surface unzone #2
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #1/C
Alignment identifier is 2
> sequence chain #13/A #13/B #13/C
Alignment identifier is 3
> ui tool show "Show Sequence Viewer"
> sequence chain #13/A #13/B #13/C
Alignment identifier is 2
> hide #!1 models
> hide #!2 models
> show #!6 models
> show #!4 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select add #1
27102 atoms, 27867 bonds, 6 pseudobonds, 3399 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!4 models
> show #!4 models
> show #!6 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6 models
Drag select of 181 atoms, 180 pseudobonds
> show #!6 models
> ui tool show "Color Zone"
> color zone #6.2 near #4 distance 8.3
> volume splitbyzone #6.2
Opened 103_zflipped.ccp4 1 0 as #9.1, grid size 300,300,300, pixel 1.38, shown
at level 0.19, step 1, values float32
Opened 103_zflipped.ccp4 1 1 as #9.2, grid size 300,300,300, pixel 1.38, shown
at level 0.19, step 1, values float32
> hide #!9.1 models
> show #!9.1 models
> close #9.1
> hide #!6 models
> show #!6 models
> close #6
> hide #!9.2 models
> show #!9.2 models
> color #9.2 #55627080 models
> select clear
Drag select of 9.2 103_zflipped.ccp4 1 1 , 34 atoms, 36 pseudobonds
> cofr sel
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:366
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/A:366
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/A:366,369
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #4/A:338,366,369
33 atoms, 33 bonds, 3 residues, 1 model selected
> select #4/A:338,366,369
33 atoms, 33 bonds, 3 residues, 1 model selected
> select clear
> show #!4 cartoons
> select #4/A:338
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/A:338
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/A:338,366
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #4/A:352
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:352
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:327,352
12 atoms, 11 bonds, 2 residues, 1 model selected
Drag select of 9.2 103_zflipped.ccp4 1 1 , 1 residues
> select #4/A:327-328
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #4/A:327-328
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #4/A:328
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:327-328
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #4/A:327
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:327
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:327,352
12 atoms, 11 bonds, 2 residues, 1 model selected
> toolshed show
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> open
> /Users/kelvinlau/Downloads/clustalo-I20260401-175019-0503-45788964-p1m.aln-
> clustal_num
Unrecognized file suffix '.aln-clustal_num'
> open
> /Users/kelvinlau/Downloads/clustalo-I20260401-175019-0503-45788964-p1m.aln
Summary of feedback from opening
/Users/kelvinlau/Downloads/clustalo-I20260401-175019-0503-45788964-p1m.aln
---
notes | Alignment identifier is clustalo-I20260401-175019-0503-45788964-p1m.aln
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain A to rhgb07 with 0 mismatches
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain B to rhgb07 with 0 mismatches
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain C to rhgb07 with 0 mismatches
Associated 30B-RBD-only.pdb chain A to rhgb07 with 4 mismatches
Associated 8u29 chain A to rhgb07 with 95 mismatches
Associated 8u29 chain B to rhgb07 with 95 mismatches
Associated 8u29 chain C to rhgb07 with 95 mismatches
Associated 8u29 chain A to rhgb07 with 95 mismatches
Associated sarscov2closed chain A to cov2 with 1 mismatch
Associated sarscov2closed chain B to cov2 with 1 mismatch
Associated sarscov2closed chain C to cov2 with 1 mismatch
Showing conservation header ("seq_conservation" residue attribute) for
alignment clustalo-I20260401-175019-0503-45788964-p1m.aln
Opened 2 sequences from clustalo-I20260401-175019-0503-45788964-p1m.aln
> select #13/A-C:336
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #13/A-C:336
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #13/A-C:336 #1/A-C:327 #4/A:327 #5/A-C:326 #8/A:326
66 atoms, 55 bonds, 11 residues, 5 models selected
> select #13/A-C:336 #1/A-C:327 #4/A:327 #5/A-C:326 #8/A:326
66 atoms, 55 bonds, 11 residues, 5 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region cov2..rhgb07 [336]
RMSD: 1.201
> select #13/A-C:336,361 #1/A-C:327,352 #4/A:327,352 #5/A-C:326,351
> #8/A:326,351
132 atoms, 121 bonds, 22 residues, 5 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 1.110
> select #13/A-C:336,341,361 #1/A-C:327,332,352 #4/A:327,332,352
> #5/A-C:326,331,351 #8/A:326,331,351
209 atoms, 187 bonds, 33 residues, 5 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 1.017
> select #13/A-C:336,341-342,361 #1/A-C:327,332-333,352 #4/A:327,332-333,352
> #5/A-C:326,331-332,351 #8/A:326,331-332,351
330 atoms, 319 bonds, 2 pseudobonds, 44 residues, 7 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 1.017
> select #13/A-C:336,338,341-342,361 #1/A-C:327,329,332-333,352
> #4/A:327,329,332-333,352 #5/A-C:326,328,331-332,351 #8/A:326,328,331-332,351
451 atoms, 440 bonds, 2 pseudobonds, 55 residues, 7 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 1.058
> select #13/A-C:336,338,341-342,361,374 #1/A-C:327,329,332-333,352,366
> #4/A:327,329,332-333,352,366 #5/A-C:326,328,331-332,351,365
> #8/A:326,328,331-332,351,365
572 atoms, 561 bonds, 2 pseudobonds, 66 residues, 7 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 1.137
> select #13/A-C:336,338,341-342,361,374,377
> #1/A-C:327,329,332-333,352,366,369 #4/A:327,329,332-333,352,366,369
> #5/A-C:326,328,331-332,351,365,368 #8/A:326,328,331-332,351,365,368
693 atoms, 682 bonds, 2 pseudobonds, 77 residues, 7 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 1.157
> select #13/A-C:336,338,341-342,361,374,377,392
> #1/A-C:327,329,332-333,352,366,369,384 #4/A:327,329,332-333,352,366,369,384
> #5/A-C:326,328,331-332,351,365,368,383 #8/A:326,328,331-332,351,365,368,383
814 atoms, 803 bonds, 2 pseudobonds, 88 residues, 7 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 1.159
> select #13/A-C:336,338,341-342,361,374,377,392,515
> #1/A-C:327,329,332-333,352,366,369,384,503
> #4/A:327,329,332-333,352,366,369,384,503
> #5/A-C:326,328,331-332,351,365,368,383,502
> #8/A:326,328,331-332,351,365,368,383,502
923 atoms, 908 bonds, 2 pseudobonds, 99 residues, 7 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 1.374
> select #13/A-C:336,338,341-342,361,374,377,379,392,515
> #1/A-C:327,329,332-333,352,366,369,371,384,503
> #4/A:327,329,332-333,352,366,369,371,384,503
> #5/A-C:326,328,331-332,351,365,368,370,383,502
> #8/A:326,328,331-332,351,365,368,370,383,502
989 atoms, 963 bonds, 2 pseudobonds, 110 residues, 7 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 2.012
> select #13/A-C:336,338,341-342,361,374,377,379,392,432,515
> #1/A-C:327,329,332-333,352,366,369,371,384,424,503
> #4/A:327,329,332-333,352,366,369,371,384,424,503
> #5/A-C:326,328,331-332,351,365,368,370,383,423,502
> #8/A:326,328,331-332,351,365,368,370,383,423,502
1055 atoms, 1029 bonds, 2 pseudobonds, 121 residues, 7 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 1.933
> select #13/A-C:336,338,341-342,361,374,377,379,392,432,436,515
> #1/A-C:327,329,332-333,352,366,369,371,384,424,428,503
> #4/A:327,329,332-333,352,366,369,371,384,424,428,503
> #5/A-C:326,328,331-332,351,365,368,370,383,423,427,502
> #8/A:326,328,331-332,351,365,368,370,383,423,427,502
1209 atoms, 1194 bonds, 2 pseudobonds, 132 residues, 7 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection
RMSD: 1.868
> select #4/A:327,329,332-333,352,366,369,371,384,424,428,503
111 atoms, 110 bonds, 12 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 111 atom styles
> ui tool show "Color Actions"
> color sel #b44e66ff target a
> color sel byhetero target a
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select clear
> select #1/A-C:327,329,332-333,352,366,369,371,384,424,428,503
333 atoms, 330 bonds, 36 residues, 1 model selected
> show #!4 atoms
> hide #!4 atoms
> hide #!4 models
> show #!1 models
> select add #1
27102 atoms, 27867 bonds, 6 pseudobonds, 3399 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/A:327,329,332-333,352,366,369,371,384,424,428,503
111 atoms, 110 bonds, 12 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 111 atom styles
> color sel #5272aaff target a
> color sel #b44e66ff target a
> color sel byhetero target a
> select #1/B:408-409
11 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> hide sel atoms
> select #1/B:399-400
16 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> hide sel atoms
> select #1/A-C:400 #4/A:400 #5/A-C:399 #8/A:399
80 atoms, 72 bonds, 8 residues, 4 models selected
> select #1/A-C:400-401 #4/A:400-401 #5/A-C:399-400 #8/A:399-400
152 atoms, 144 bonds, 1 pseudobond, 16 residues, 5 models selected
clustalo-I20260401-175019-0503-45788964-p1m.aln [ID:
clustalo-I20260401-175019-0503-45788964-p1m.aln] region rhgb07 [409-410] RMSD:
0.884
> show sel & #!1 atoms
> hide sel & #!1 atoms
> select #1/B:400-401
18 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> color sel #5272aaff target a
> color sel #b44e66ff target a
> color sel byhetero target a
> select clear
> ui tool show "Side View"
> volume #9.2 level 0.1611
> volume #9.2 level 0.2606
> volume #9.2 level 0.1873
> select add #1/A:356
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select clear
> select add #1/A:356@CD1
1 atom, 1 residue, 1 model selected
> select subtract #1/A:356
Nothing selected
> select add #1/A:356
12 atoms, 12 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel #5272aaff target a
> color sel #b44e66ff target a
> color sel byhetero target a
> select clear
> volume #9.2 level 0.2475
Drag select of 9.2 103_zflipped.ccp4 1 1 , 3 residues, 1 bonds
> select clear
Drag select of 1 atoms
> select clear
> save /Users/kelvinlau/Desktop/image2.png supersample 3
> save /Users/kelvinlau/Desktop/RhGB07-full/v7/rbd-lipid.cxs includeMaps true
===== Log before crash end =====
Log:
> graphics silhouettes true
> lighting soft
> windowsize 800 800
> ui tool hide "command line interface"
> ui tool show clix
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Max
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: MacBookPro18,4
Model Number: Z15H00063SM/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 Performance and 2 Efficiency)
Memory: 32 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (a) (25D771280a)
Kernel Version: Darwin 25.3.0
Time since boot: 5 days, 18 hours, 31 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
DELL S2722QC:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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-clix: 0.2.5
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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