![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17912 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.0-arm64-arm-64bit
ChimeraX Version: 1.9.dev202406122300 (2024-06-12 23:00:04 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020e86a500 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, psutil._psutil_osx, psutil._psutil_posix, chimerax.morph._morph, chimerax.coulombic._esp (total: 64)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 1543,
"osVersion" : {
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"build" : "22A380",
"releaseType" : "User"
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"captureTime" : "2025-06-05 15:28:34.6554 +0900",
"incident" : "A27F065C-EEBF-4735-818A-BD165D420581",
"pid" : 42289,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-05 11:31:36.2864 +0900",
"procStartAbsTime" : 12281917756085,
"procExitAbsTime" : 12622877752299,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"A694AF0A-44F0-5280-8548-64CD76211319","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BAD2AE41-161A-1B52-2311-32EA41EAEBF4",
"wakeTime" : 8,
"sleepWakeUUID" : "CAB26E84-C871-42D8-8AE1-12332401D6A0",
"sip" : "enabled",
"vmRegionInfo" : "0x58341929de48 is not in any region. Bytes after previous region: 96499747380809 Bytes before following region: 8572332548536\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000d8341929de48","rawCodes":[1,237718272073288],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000d8341929de48 -> 0x000058341929de48 (possible pointer authentication failure)"},
"vmregioninfo" : "0x58341929de48 is not in any region. Bytes after previous region: 96499747380809 Bytes before following region: 8572332548536\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.9.dev202406122300 (2024-06-12)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/uijin/Desktop/GTR1_Map and Models/Pontus
> Gourdon/GTR1_apo_IF_8.0/Gtr1_apo.pdb" format pdb
Chain information for Gtr1_apo.pdb #1
---
Chain | Description
A | No description available
> open "/Users/uijin/Desktop/GTR1_Map and
> Models/GTR1I_6.0_IF/GTR1I_6.0_IF.pdb" format pdb
Chain information for GTR1I_6.0_IF.pdb #2
---
Chain | Description
B | No description available
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Map and
> Models/GTR1M_6.0_OCC_full/GTR1M_6.0_OCC_full_pre-model.pdb" format pdb
Chain information for GTR1M_6.0_OCC_full_pre-model.pdb #3
---
Chain | Description
B | No description available
> matchmaker #3 to #2
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 GTR1I_6.0_IF.pdb, chain B (#2) with GTR1M_6.0_OCC_full_pre-
model.pdb, chain B (#3), sequence alignment score = 2627.4
RMSD between 446 pruned atom pairs is 0.924 angstroms; (across all 532 pairs:
2.099)
> close #1
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Map and
> Models/GTR1A_OCC_7.5_V/GTR1A_OCC_7.5.pdb" format pdb
Chain information for GTR1A_OCC_7.5.pdb #1
---
Chain | Description
A | No description available
> matchmaker #1 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 GTR1M_6.0_OCC_full_pre-model.pdb, chain B (#3) with
GTR1A_OCC_7.5.pdb, chain A (#1), sequence alignment score = 2618.5
RMSD between 319 pruned atom pairs is 0.948 angstroms; (across all 527 pairs:
3.080)
> hide #!1 models
> show #!1 models
> hide #2 models
> rename #3 id #2
> show #!2 models
> hide #!2 target m
> close #2
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Map and
> Models/GTR1M_6.0_OCC_full/GTR1M_6.0_OCC_full_pre-model.pdb" format pdb
Chain information for GTR1M_6.0_OCC_full_pre-model.pdb #2
---
Chain | Description
B | No description available
> open "/Users/uijin/Desktop/GTR1_Map and
> Models/GTR1I_6.0_IF/GTR1I_6.0_IF.pdb" format pdb
Chain information for GTR1I_6.0_IF.pdb #3
---
Chain | Description
B | No description available
> matchmaker #2-3 to #1
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 GTR1A_OCC_7.5.pdb, chain A (#1) with GTR1M_6.0_OCC_full_pre-
model.pdb, chain B (#2), sequence alignment score = 2618.5
RMSD between 319 pruned atom pairs is 0.948 angstroms; (across all 527 pairs:
3.080)
Matchmaker GTR1A_OCC_7.5.pdb, chain A (#1) with GTR1I_6.0_IF.pdb, chain B
(#3), sequence alignment score = 2679.5
RMSD between 279 pruned atom pairs is 0.797 angstroms; (across all 531 pairs:
4.416)
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #3 models
> hide #!2 models
> show #!2 models
> rainbow
> show #3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Map and Models/Pontus
> Gourdon/GTR3_I3M_IF_6.5 /Gtr3_pH6.5.pdb"
Chain information for Gtr3_pH6.5.pdb #4
---
Chain | Description
A | No description available
> 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 GTR1I_6.0_IF.pdb, chain B (#3) with Gtr3_pH6.5.pdb, chain A (#4),
sequence alignment score = 2117.8
RMSD between 470 pruned atom pairs is 0.967 angstroms; (across all 540 pairs:
1.885)
> rainbow
> hide #!1 models
> hide #!2 models
> show atoms
> color byhetero
> hide #250-1000 atoms
> hide :300-1000 atoms
> hide H
> show atoms
> hide H
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Map and Models/Pontus
> Gourdon/GTR3_apo_OCC_8.0 /Gtr3_apo.pdb"
Chain information for Gtr3_apo.pdb #5
---
Chain | Description
A | No description available
> matchmaker #5 to #1
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 GTR1A_OCC_7.5.pdb, chain A (#1) with Gtr3_apo.pdb, chain A (#5),
sequence alignment score = 1812.2
RMSD between 335 pruned atom pairs is 1.106 angstroms; (across all 489 pairs:
2.702)
> rainbow
> show atoms
> hide H
> color byhetero
> hide #3 models
> hide #!4 models
> show #!1 models
> hide #!5 models
> hide atoms
> show :513 atoms
> show #!2 models
> show #3 models
> hide H
> hide #3 models
> show #3 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> select :513
48 atoms, 43 bonds, 5 residues, 5 models selected
> hbonds sel & #3#!1-2 reveal true
57 hydrogen bonds found
> select clear
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> open /Users/uijin/Downloads/cryosparc_P3_J2119_008_volume_map_sharp.mrc
Opened cryosparc_P3_J2119_008_volume_map_sharp.mrc as #7, grid size
240,240,240, pixel 0.901, shown at level 0.0468, step 1, values float32
> hide #!1 models
> hide #!2 models
> hide #3 models
> hide #6 models
> volume #7 level 0.1567
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Map and
> Models/Updates_Jan2025/GTR1_apo_6.0_Jan2025.pdb"
Chain information for GTR1_apo_6.0_Jan2025.pdb #8
---
Chain | Description
A | No description available
> ui tool show "Fit in Map"
> fitmap #8 inMap #7
Fit molecule GTR1_apo_6.0_Jan2025.pdb (#8) to map
cryosparc_P3_J2119_008_volume_map_sharp.mrc (#7) using 4105 atoms
average map value = 0.1642, steps = 108
shifted from previous position = 1.84
rotated from previous position = 11.6 degrees
atoms outside contour = 2129, contour level = 0.15666
Position of GTR1_apo_6.0_Jan2025.pdb (#8) relative to
cryosparc_P3_J2119_008_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.99211889 0.09596544 -0.08056509 -1.71671143
-0.10749464 0.98224775 -0.15373439 31.01798183
0.06438169 0.16118311 0.98482232 -23.37018498
Axis 0.78343842 -0.36059247 -0.50615938
Axis point 0.00000000 164.25022773 181.15325648
Rotation angle (degrees) 11.59451868
Shift along axis -0.70075007
> save 2119.pdb #8
> open /Users/uijin/Downloads/cryosparc_P3_J2128_007_volume_map_sharp.mrc
Opened cryosparc_P3_J2128_007_volume_map_sharp.mrc as #9, grid size
240,240,240, pixel 0.901, shown at level 0.0481, step 1, values float32
> hide #!7 models
> volume #9 level 0.1991
> select add #8
4105 atoms, 4213 bonds, 1 pseudobond, 522 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.90352,-0.42705,-0.035751,250.27,0.40729,-0.88166,0.23832,124.26,-0.13329,0.20076,0.97053,-4.6786
> fitmap #8 inMap #9
Fit molecule GTR1_apo_6.0_Jan2025.pdb (#8) to map
cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) using 4105 atoms
average map value = 0.0485, steps = 108
shifted from previous position = 3.55
rotated from previous position = 3.99 degrees
atoms outside contour = 3481, contour level = 0.19908
Position of GTR1_apo_6.0_Jan2025.pdb (#8) relative to
cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
-0.87673545 -0.48056076 -0.01990761 253.58996440
0.46640071 -0.85955529 0.20889013 120.88438925
-0.11749609 0.17385645 0.97773647 -2.50031376
Axis -0.03677608 0.10244208 0.99405892
Axis point 111.34532317 92.90248942 0.00000000
Rotation angle (degrees) 151.55528712
Shift along axis 0.57214246
> view matrix models
> #8,-0.9716,-0.2366,0.0031723,236.23,0.23529,-0.96464,0.11875,166.26,-0.025035,0.11612,0.99292,-8.1467
> fitmap #8 inMap #9
Fit molecule GTR1_apo_6.0_Jan2025.pdb (#8) to map
cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) using 4105 atoms
average map value = 0.08762, steps = 88
shifted from previous position = 5.96
rotated from previous position = 10.4 degrees
atoms outside contour = 3174, contour level = 0.19908
Position of GTR1_apo_6.0_Jan2025.pdb (#8) relative to
cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
-0.99500932 -0.08273165 -0.05578467 226.80069626
0.07110080 -0.98009858 0.18534145 183.16152629
-0.07000808 0.18045014 0.98108950 -11.41175418
Axis -0.03164547 0.09202158 0.99525403
Axis point 109.65489745 96.51674693 0.00000000
Rotation angle (degrees) 175.56759009
Shift along axis -1.67999608
> view matrix models
> #8,-0.9433,-0.33186,-0.0070666,241.5,0.33128,-0.93988,-0.08287,180.35,0.02086,-0.080512,0.99654,3.9235
> fitmap #8 inMap #9
Fit molecule GTR1_apo_6.0_Jan2025.pdb (#8) to map
cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) using 4105 atoms
average map value = 0.2092, steps = 128
shifted from previous position = 6.21
rotated from previous position = 19.3 degrees
atoms outside contour = 2170, contour level = 0.19908
Position of GTR1_apo_6.0_Jan2025.pdb (#8) relative to
cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
-0.99736419 -0.06329504 -0.03547412 227.44034456
0.05928203 -0.99274712 0.10458872 196.60738048
-0.04183677 0.10221006 0.99388268 -6.35153927
Axis -0.01937564 0.05182788 0.99846805
Axis point 110.63355249 101.96724162 0.00000000
Rotation angle (degrees) 176.48082563
Shift along axis -0.55886767
> fitmap #8 inMap #9
Fit molecule GTR1_apo_6.0_Jan2025.pdb (#8) to map
cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) using 4105 atoms
average map value = 0.2092, steps = 28
shifted from previous position = 0.0213
rotated from previous position = 0.0115 degrees
atoms outside contour = 2172, contour level = 0.19908
Position of GTR1_apo_6.0_Jan2025.pdb (#8) relative to
cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
-0.99736364 -0.06320680 -0.03564636 227.43030336
0.05917890 -0.99275909 0.10453345 196.61889004
-0.04199547 0.10214835 0.99388233 -6.33353919
Axis -0.01945853 0.05179842 0.99846797
Axis point 110.63299349 101.96680718 0.00000000
Rotation angle (degrees) 176.48632640
Shift along axis -0.56474702
> save 2128.pdb #8
> close #8-9
> show #!7 models
> close #7
> show #6 models
> show #!1 models
> hide #6 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Map and
> Models/Updates_Jan2025/GTR1_apo_6.0_Jan2025.pdb"
Chain information for GTR1_apo_6.0_Jan2025.pdb #7
---
Chain | Description
A | No description available
> matchmaker #7 to #2
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 GTR1M_6.0_OCC_full_pre-model.pdb, chain B (#2) with
GTR1_apo_6.0_Jan2025.pdb, chain A (#7), sequence alignment score = 2510
RMSD between 274 pruned atom pairs is 0.994 angstroms; (across all 514 pairs:
4.408)
> rainbow
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> morph #7 #2
Computed 51 frame morph #8
> coordset #8 1,51
> rainbow
> show #1-100 atoms
> ubdo
Unknown command: ubdo
> ubdo
Unknown command: ubdo
> undo
> show :1-100 atoms
> color byhetero
> select #8:1-100 atoms
Expected a keyword
> select #8:1-100
289 atoms, 295 bonds, 36 residues, 1 model selected
> hbonds sel reveal true
209 hydrogen bonds found
> show #6 models
> select clear
> show :196 atoms
> hide #6 models
> show #6 models
> show #3 models
> hide H
> morph #8 #2 #3
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/morph/morph.py", line 84, in morph
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/morph/motion.py", line 28, in compute_morph
motion.interpolate(res_groups, atom_map, res_interp)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
IndexError: index 4031 is out of bounds for axis 0 with size 4031
IndexError: index 4031 is out of bounds for axis 0 with size 4031
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/morph/motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
> hide #3 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!7 models
> morph #7 #2 #3
Computed 101 frame morph #9
> coordset #9 1,101
> hide #!8 models
> rainbow
> show :196 atoms
> show :1-100 atoms
> color byhetero
> select :1-100
3293 atoms, 3362 bonds, 151 pseudobonds, 400 residues, 9 models selected
> hbonds sel & #!9 reveal true
230 hydrogen bonds found
> select clear
> morph #7 #3
Computed 51 frame morph #10
> coordset #10 1,51
> hide #!9 models
> color byhetero
> rainbow
> color byhetero
> select :1-100
3624 atoms, 3700 bonds, 166 pseudobonds, 441 residues, 10 models selected
> hbonds sel & #!10 reveal true
299 hydrogen bonds found
> select clear
> select :86
78 atoms, 69 bonds, 9 residues, 9 models selected
> interfaces select & #!10 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & #!10 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> show :111
> show :115
> hide #!10 models
> show #!9 models
> open 7nqk
Summary of feedback from opening 7nqk fetched from pdb
---
note | Fetching compressed mmCIF 7nqk from http://files.rcsb.org/download/7nqk.cif
7nqk title:
Cryo-EM structure of the mammalian peptide transporter PepT2 [more info...]
Chain information for 7nqk #11
---
Chain | Description | UniProt
A | Solute carrier family 15 member 2 | S15A2_RAT 1-729
B | nanobody |
> matchmaker #11 to #1
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 GTR1A_OCC_7.5.pdb, chain A (#1) with 7nqk, chain A (#11), sequence
alignment score = 600.4
RMSD between 209 pruned atom pairs is 1.228 angstroms; (across all 466 pairs:
7.209)
> rainbow
> hide #!9 models
> show #!1 models
> hide #!1 models
> show #11:87 atoms
> open 2xut
Summary of feedback from opening 2xut fetched from pdb
---
note | Fetching compressed mmCIF 2xut from http://files.rcsb.org/download/2xut.cif
2xut title:
Crystal structure of a proton dependent oligopeptide (POT) family transporter.
[more info...]
Chain information for 2xut #12
---
Chain | Description | UniProt
A B C | PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN | Q8EKT7_SHEON 1-516
2xut mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> matchmaker #12 to #11
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 7nqk, chain A (#11) with 2xut, chain B (#12), sequence alignment
score = 651.5
RMSD between 124 pruned atom pairs is 0.978 angstroms; (across all 408 pairs:
11.501)
> rainbow
> hide #11 models
> show #11 models
> hide #!12 models
> show #!12 models
> hide #11 models
> show #12:61 atoms
> coulombic #!12
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2xut_A SES surface #12.2: minimum, -15.80, mean 0.12,
maximum 15.66
Coulombic values for 2xut_B SES surface #12.3: minimum, -15.98, mean 0.10,
maximum 14.99
Coulombic values for 2xut_C SES surface #12.4: minimum, -15.69, mean 0.13,
maximum 15.76
To also show corresponding color key, enter the above coulombic command and
add key true
> view
> ui tool show "Side View"
> delete #12/A/B
> hide #!12 surfaces
> show #12:61 atoms
> show #!12 surfaces
> hide #!12 surfaces
> show #!12 surfaces
> hide #!12 surfaces
> show #!12 surfaces
> close #12
> show #11 models
> hide #11 models
> show #!9 models
> color byhetero
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9.dev202406122300 (2024-06-12)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11C001DKKH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.41.10
OS Loader Version: 8419.41.10
Software:
System Software Overview:
System Version: macOS 13.0 (22A380)
Kernel Version: Darwin 22.1.0
Time since boot: 22 days, 6 hours, 22 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LS32A600U:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.13
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.2
ChimeraX-AtomicLibrary: 14.1.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9.dev202406122300
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-DeepMutationalScan: 1.0
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.4
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.1.5
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.12.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.6
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.32.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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