![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15776 closed defect (duplicate)
Crash waking Mac up 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-13.6.7-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00000001f6e7e100 (most recent call first):
File "/Applications/ChimeraX-1.8.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-1.8.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-1.8.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.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.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, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)
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{
"uptime" : 280000,
"procRole" : "Background",
"version" : 2,
"userID" : 416321282,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 14837,
"osVersion" : {
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"build" : "22G720",
"releaseType" : "User"
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"captureTime" : "2024-08-17 11:42:30.9906 -0400",
"incident" : "B2E1C708-8652-49CD-B091-373075FFE7ED",
"pid" : 70478,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-16 20:37:53.2256 -0400",
"procStartAbsTime" : 6679438633612,
"procExitAbsTime" : 6931008305330,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5B8D8112-BB23-50D9-92B5-EAF65637AA80","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "75718223-CFE9-3FB0-AD07-211080835B57",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 3,
"sleepWakeUUID" : "D6632687-28B4-4EEC-9AAB-9F0D755EB073",
"sip" : "enabled",
"vmRegionInfo" : "0x5162d2f04798 is not in any region. Bytes after previous region: 89003851270041 Bytes before following region: 16068228659304\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, 0x00005162d2f04798","rawCodes":[1,89484887607192],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00005162d2f04798"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":70478},
"vmregioninfo" : "0x5162d2f04798 is not in any region. Bytes after previous region: 89003851270041 Bytes before following region: 16068228659304\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: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/Rilee EC MgtA Paper
> Structures/Paper PDB
> Structures/monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb"
monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb title:
Magnesium transporter MGTA monomer from E. Coli In 5 MM MGCL2 [more info...]
Chain information for
monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb #1
---
Chain | Description | UniProt
A | magnesium-transporting atpase, P-type 1 | ATMA_ECOLI 1-898
Non-standard residues in
monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb #1
---
MG — magnesium ion
> set bgColor white
> lighting flat
> lighting shadows true intensity 0.5
> select #1/A:95-115
164 atoms, 167 bonds, 21 residues, 1 model selected
> select #1/A:95-137
326 atoms, 331 bonds, 43 residues, 1 model selected
> select #1/A:1-95
344 atoms, 353 bonds, 62 residues, 1 model selected
> select #1/A:1-90
300 atoms, 306 bonds, 57 residues, 1 model selected
> select #1/A:1-85
271 atoms, 275 bonds, 52 residues, 1 model selected
> select #1/A:1-86
278 atoms, 283 bonds, 53 residues, 1 model selected
> select #1/A:87-115
223 atoms, 230 bonds, 29 residues, 1 model selected
> select #1/A:87-137
385 atoms, 394 bonds, 51 residues, 1 model selected
> select #1/A:87-140
404 atoms, 413 bonds, 54 residues, 1 model selected
> select #1/A:87-142
415 atoms, 424 bonds, 56 residues, 1 model selected
> select #1/A:87-145
430 atoms, 439 bonds, 59 residues, 1 model selected
> ui tool show "Color Actions"
> color sel silver
> color sel gray
> select /A:279
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:146-278
675 atoms, 682 bonds, 133 residues, 1 model selected
> select #1/A:279-388
844 atoms, 857 bonds, 110 residues, 1 model selected
> select #1/A:279-335
441 atoms, 451 bonds, 57 residues, 1 model selected
> color sel burly wood
> color sel goldenrod
> color sel sienna
> color sel chocolate
> color sel dark goldenrod
> color sel goldenrod
> color sel sandy brown
> color sel sienna
> color sel brown
> color sel chocolate
> color sel saddle brown
> color sel peru
> color sel dark goldenrod
> color sel dark khaki
> color sel dark salmon
> color sel dark red
> color sel maroon
> color sel sienna
> color sel indian red
> color sel goldenrod
> color sel dark goldenrod
> color sel peru
> color sel dark goldenrod
> select /A:349
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:279-349
539 atoms, 549 bonds, 71 residues, 1 model selected
> color sel dark goldenrod
> select #1/A:279-350
548 atoms, 558 bonds, 72 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark goldenrod
> select #1/A:351-400
382 atoms, 384 bonds, 50 residues, 1 model selected
> select #1/A:351-375
194 atoms, 195 bonds, 25 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep sky blue
> color sel medium turquoise
> color sel cornflower blue
> select #1/A:376-450
519 atoms, 527 bonds, 75 residues, 1 model selected
> select #1/A:376-550
1201 atoms, 1216 bonds, 175 residues, 1 model selected
> select #1/A:376-549
1194 atoms, 1209 bonds, 174 residues, 1 model selected
> color sel crimson
> color sel dark red
> color sel fire brick
> color sel red
> color sel orange red
> color sel crimson
> select #1/A:550-600
355 atoms, 356 bonds, 51 residues, 1 model selected
> select #1/A:550-650
746 atoms, 753 bonds, 101 residues, 1 model selected
> select #1/A:550-700
1124 atoms, 1133 bonds, 151 residues, 1 model selected
> select #1/A:550-765
1639 atoms, 1663 bonds, 216 residues, 1 model selected
> select #1/A:550-665
842 atoms, 849 bonds, 116 residues, 1 model selected
> select #1/A:550-675
921 atoms, 928 bonds, 126 residues, 1 model selected
> color sel cornflower blue
> select #1/A:550-690
1039 atoms, 1046 bonds, 141 residues, 1 model selected
> color sel cornflower blue
> select #1/A:690-745
440 atoms, 451 bonds, 56 residues, 1 model selected
> select #1/A:690-748
467 atoms, 479 bonds, 59 residues, 1 model selected
> color sel midnight blue
> color sel black
> color sel dim gray
> color sel black
> color sel dim gray
> select #1/A:87-145
430 atoms, 439 bonds, 59 residues, 1 model selected
> color sel light gray
> color sel gray
> color sel dim gray
> color sel gray
> ui tool show "Color Actions"
> color sel pale violet red
> color sel orchid
> color sel thistle
> color sel plum
> color sel light pink
> color sel thistle
> color sel pale violet red
> color sel orchid
> color sel plum
> color sel orchid
> color sel pale violet red
> color sel violet
> color sel plum
> color sel violet
> select #1/A:690-748
467 atoms, 479 bonds, 59 residues, 1 model selected
> color sel gray
> select #1/A:749-886
1118 atoms, 1155 bonds, 138 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark gray
> color sel dim gray
> color sel dark gray
> color sel dim gray
> color sel dark gray
> color sel dim gray
> select #1/A:690-748
467 atoms, 479 bonds, 59 residues, 1 model selected
> color sel dark gray
> select clear
> select #1/A:749-889
1138 atoms, 1175 bonds, 141 residues, 1 model selected
> select #1/A:749-891
1161 atoms, 1200 bonds, 143 residues, 1 model selected
> select #1/A:749-892
1167 atoms, 1206 bonds, 144 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dim gray
> select clear
> save "/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/monomer_apo_Mg_C2nosymm_colorcoded_fig.png" width 1152
> height 765 supersample 3 transparentBackground true
> select #1/A:690-748
467 atoms, 479 bonds, 59 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dim gray
> select #1/A:749-892
1167 atoms, 1206 bonds, 144 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark gray
> select clear
> save "/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/monomer_apo_Mg_C2nosymm_colorcoded_fig.png" width 1152
> height 765 supersample 3 transparentBackground true
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/Rilee EC MgtA Paper
> Structures/Paper PDB
> Structures/dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb"
dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb title:
Magnesium transporter MGTA dimer from E. Coli In 5 MM MGCL2 [more info...]
Chain information for dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb
#2
---
Chain | Description | UniProt
A B | magnesium-transporting atpase, P-type 1 | ATMA_ECOLI 1-898
Non-standard residues in
dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb #2
---
MG — magnesium ion
> hide #!1 models
> select #1/A:87-145 color sel violet
Expected a keyword
> select #1/A:87-145, color sel violet
Expected a keyword
> select #1/A:87-145
430 atoms, 439 bonds, 59 residues, 1 model selected
> select #2/A:87-145
467 atoms, 480 bonds, 59 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> select #2/A:87-145 color sel red
Expected a keyword
> select #2/A:87-145, color sel red
Expected a keyword
> ui tool show "Color Actions"
> color sel rebecca purple
> open /Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/ChimeraX/PType_ATPases_Color.cxc
> select #2/A:1-86
642 atoms, 659 bonds, 86 residues, 1 model selected
> select #2/A:87-145 (violet)
Expected a keyword
> open /Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/ChimeraX/PType_ATPases_Color.cxc
> select #2/A:1-86
642 atoms, 659 bonds, 86 residues, 1 model selected
> select #2/A:87-145
467 atoms, 480 bonds, 59 residues, 1 model selected
> color sel violet
> select #2/A:146-278
949 atoms, 963 bonds, 133 residues, 1 model selected
> select #2/A:279-350
548 atoms, 558 bonds, 72 residues, 1 model selected
> color sel dark goldenrod
> select #2/A:351-375
194 atoms, 195 bonds, 25 residues, 1 model selected
> color sel cornflower blue
> select #2/A:376-549
1389 atoms, 1410 bonds, 174 residues, 1 model selected
> color sel crimson
> select #2/A:550-690
1039 atoms, 1046 bonds, 141 residues, 1 model selected
> color sel cornflower blue
> select #2/A:690-748
467 atoms, 479 bonds, 59 residues, 1 model selected
> color sel dim gray
> select #2/A:749-892
1167 atoms, 1206 bonds, 144 residues, 1 model selected
> color sel dark gray
executed PType_ATPases_Color.cxc
> select #2/A:1-86
642 atoms, 659 bonds, 86 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> color sel gold
> color sel dark orange
> color sel orange
> color sel goldenrod
> color sel sandy brown
> hide #!2 models
> show #!1 models
> select clear
> select #1/A:259
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!2 models
> color sel pale goldenrod
> color sel khaki
> select #2/A:1-86
642 atoms, 659 bonds, 86 residues, 1 model selected
> color sel pale goldenrod
> color sel khaki
> color sel wheat
> color sel beige
> color sel antique white
> color sel light goldenrod yellow
> color sel old lace
> color sel peach puff
> color sel navajo white
> color sel moccasin
> color sel bisque
> color sel misty rose
> color sel blanched almond
> color sel papaya whip
> color sel lemon chiffon
> hide #!2 models
> show #!1 models
> select #1
5982 atoms, 6094 bonds, 1 pseudobond, 860 residues, 2 models selected
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel list
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #1/A:259
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:259
4 atoms, 3 bonds, 1 residue, 1 model selected
> view #2 clip false
Drag select of 168 residues
> select clear
Drag select of 90 residues
> ui tool show "Color Actions"
> color sel tan
> color sel burly wood
> color sel light coral
> color sel tan
> color sel burly wood
> color sel tan
> select clear
> hide #!1 models
> show #!2 models
> open /Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/ChimeraX/PType_ATPases_Color.cxc
> select #2/A:1-86
642 atoms, 659 bonds, 86 residues, 1 model selected
> color sel tan
> select #2/A:87-145
467 atoms, 480 bonds, 59 residues, 1 model selected
> color sel violet
> select #2/A:146-278
949 atoms, 963 bonds, 133 residues, 1 model selected
> color sel tan
> select #2/A:279-350
548 atoms, 558 bonds, 72 residues, 1 model selected
> color sel dark goldenrod
> select #2/A:351-375
194 atoms, 195 bonds, 25 residues, 1 model selected
> color sel cornflower blue
> select #2/A:376-549
1389 atoms, 1410 bonds, 174 residues, 1 model selected
> color sel crimson
> select #2/A:550-690
1039 atoms, 1046 bonds, 141 residues, 1 model selected
> color sel cornflower blue
> select #2/A:690-748
467 atoms, 479 bonds, 59 residues, 1 model selected
> color sel dim gray
> select #2/A:749-892
1167 atoms, 1206 bonds, 144 residues, 1 model selected
> color sel dark gray
executed PType_ATPases_Color.cxc
> select #2/A:898
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:898
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B
7018 atoms, 7060 bonds, 4 pseudobonds, 1001 residues, 2 models selected
> select #2/B:899
Nothing selected
> open /Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/ChimeraX/PType_ATPases_Color.cxc
> select #2/A:1-86
642 atoms, 659 bonds, 86 residues, 1 model selected
> color sel tan
> select #2/A:87-145
467 atoms, 480 bonds, 59 residues, 1 model selected
> color sel violet
> select #2/A:146-278
949 atoms, 963 bonds, 133 residues, 1 model selected
> color sel tan
> select #2/A:279-350
548 atoms, 558 bonds, 72 residues, 1 model selected
> color sel dark goldenrod
> select #2/A:351-375
194 atoms, 195 bonds, 25 residues, 1 model selected
> color sel cornflower blue
> select #2/A:376-549
1389 atoms, 1410 bonds, 174 residues, 1 model selected
> color sel crimson
> select #2/A:550-690
1039 atoms, 1046 bonds, 141 residues, 1 model selected
> color sel cornflower blue
> select #2/A:690-748
467 atoms, 479 bonds, 59 residues, 1 model selected
> color sel dim gray
> select #2/A:749-898
1228 atoms, 1270 bonds, 150 residues, 1 model selected
> color sel dark gray
> select #2/B:1-86
642 atoms, 659 bonds, 86 residues, 1 model selected
> color sel tan
> select #2/B:87-145
467 atoms, 480 bonds, 59 residues, 1 model selected
> color sel violet
> select #2/B:146-278
952 atoms, 966 bonds, 133 residues, 1 model selected
> color sel tan
> select #2/B:279-350
548 atoms, 558 bonds, 72 residues, 1 model selected
> color sel dark goldenrod
> select #2/B:351-375
194 atoms, 195 bonds, 25 residues, 1 model selected
> color sel cornflower blue
> select #2/B:376-549
1389 atoms, 1410 bonds, 174 residues, 1 model selected
> color sel crimson
> select #2/B:550-690
1039 atoms, 1046 bonds, 141 residues, 1 model selected
> color sel cornflower blue
> select #2/B:690-748
467 atoms, 479 bonds, 59 residues, 1 model selected
> color sel dim gray
> select #2/B:749-898
1228 atoms, 1270 bonds, 150 residues, 1 model selected
> color sel dark gray
executed PType_ATPases_Color.cxc
> select ~sel & ##selected
12805 atoms, 12847 bonds, 9 pseudobonds, 1852 residues, 2 models selected
> select clear
> view orient
> ui tool show "Side View"
> toolshed show
> view
> orient
Unknown command: orient
> view orient
> ui tool show "Side View"
> view orient
> view initial #1
> view initial 0
Expected a models specifier or a keyword
> view initial
> center
Unknown command: center
> view center
Expected an objects specifier or a view name or a keyword
> ui view
Missing or invalid "layout" argument: Expected one of 'default', 'fourup',
'overunder', or 'sidebyside'
> ui view default
> ui view fourup
> ui view overunder
> ui view default
> view orient
> view matrix 1,0,0,0,0,1,0,0,0,0,1,0
Expected a keyword
> view matrix
view matrix camera 1,0,0,159.32,0,1,0,159.32,0,0,1,515.15
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models #1
Invalid "models" argument: Expected model id and 12 comma-separated numbers
> view matrix #1,1,0,0,0,0,1,0,0,0,0,1,0
Expected a keyword
> view matrix camera 1,0,0,0,0,1,0,0,0,0,1,0
> view orient
> turn
> turn y 90
> turn x 90
> turn y 90
> turn y 180
> turn y 90
> view orient
> turn
> turn x -90
> view orient
> turn x -90
> turn y 90
> view orient
> turn x 90
> view orient
> turn y 90
> turn x -90
> turn y -90
> turn z 90
> turn x -90
> save "/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/dimer_apo_Mg_C2nosymm_colorcoded_fig.png" width 1152
> height 765 supersample 3 transparentBackground true
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!2 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 monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb, chain A
(#1) with dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb, chain A
(#2), sequence alignment score = 4390.5
RMSD between 305 pruned atom pairs is 0.980 angstroms; (across all 859 pairs:
11.849)
> select #2/B
7018 atoms, 7060 bonds, 4 pseudobonds, 1001 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/A
7015 atoms, 7057 bonds, 5 pseudobonds, 1001 residues, 2 models selected
> select #21A
Expected an objects specifier or a keyword
> select #1/A
5982 atoms, 6094 bonds, 1 pseudobond, 860 residues, 2 models selected
> ui tool show "Color Actions"
> color sel alice blue
> color sel orange
> color sel tomato
> color sel chartreuse
> color sel lime green
> color sel medium sea green
> color sel medium orchid
> color sel dark orchid
> color sel medium violet red
> color sel dark orchid
> color sel dark magenta
> select #1/A:95-137,288-335,696-886
2231 atoms, 2294 bonds, 282 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!2 to #1 & sel
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 monomer_apo_Mg_C1nosymm_D_1000277101_model_annotate_P1.pdb, chain A
(#1) with dimer_apo_Mg_C2symm_D_1000274597_model_annotate_P1.pdb, chain B
(#2), sequence alignment score = 1415.7
RMSD between 190 pruned atom pairs is 0.645 angstroms; (across all 282 pairs:
3.427)
> select #2/A
7015 atoms, 7057 bonds, 5 pseudobonds, 1001 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/B
7018 atoms, 7060 bonds, 4 pseudobonds, 1001 residues, 2 models selected
> show sel cartoons
> clear select
Unknown command: clear select
> select clear
> rmsd
Missing or invalid "atoms" argument: empty atom specifier
> ui tool show Matchmaker
> ui tool show "Render/Select by Attribute"
> hide #!1 models
> show #!1 models
> ui tool show "Render/Select by Attribute"
> align
Missing or invalid "atoms" argument: empty atom specifier
> align #2 toAtoms #1
Unequal number of atoms to pair, 14033 and 5982
> ui tool show "Render/Select by Attribute"
> color byattribute a:bfactor #!1-2 target absc palette
> 12.23,blue:125.825,white:239.42,red
20015 atoms, 2862 residues, atom bfactor range 12.2 to 239
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> save "/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/dimer_apo_matchmaker_to_monomer_RMSD.png" width 1152
> height 765 supersample 3 transparentBackground true
> ui tool show "Render/Select by Attribute"
> ui tool show "Scale Bar"
> undo
> redo
> ui tool show "Surface Color"
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> save "/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/dimer_apo_matchmaker_to_monomer_RMSD.png" width 1152
> height 765 supersample 3 transparentBackground true
> ui tool show "Surface Color"
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> key blue-white-red :1.0 :0.5 :0.0
> key red-white-blue :0.0 :0.5 :1.0
> key blue-white-red :1.0 :0.5 :0.0
> key red-white-blue :0.0 :0.5 :1.0
> key red-white-blue :1 :0.5 :1.0
> key red-white-blue :1. :0.5 :1.0
> key red-white-blue :1.0 :0.5 :1.0
> key red-white-blue :1.0 :0.5 :0
> key blue-white-red :0 :0.5 :1.0
> ui mousemode right translate
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> key red-white-blue :0.0 :0.5 :0
> key red-white-blue :1 :0.5 :0
> key red-white-blue :12 :0.5 :0
> key blue-white-red :0 :0.5 :12
> key blue-white-red :0 :6 :12
> key blue-white-red :0 :6 :>12
> ui mousemode right translate
> save "/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/dimer_apo_matchmaker_to_monomer_RMSD.png" width 1152
> height 765 supersample 3 transparentBackground true
> hide #3 models
> hide #!1 models
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/MgtA/CHARMM-GUI
> Processed/dimer_apo_proteinOnly.pdb"
Chain information for dimer_apo_proteinOnly.pdb #4
---
Chain | Description
P | No description available
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/MgtS AlphaFold3
> Prediction/MgtS_AF3_CHARMMGUI.pdb"
Chain information for MgtS_AF3_CHARMMGUI.pdb #5
---
Chain | Description
L | No description available
> hide #5 models
> view
> select #4
14109 atoms, 14255 bonds, 898 residues, 1 model selected
> color sel dark gray
> ui tool show "Color Actions"
> color sel light slate gray
> color sel silver
> color sel light gray
> color sel gray
> color sel dim gray
> color sel dark gray
> color sel medium purple
> color sel pale violet red
> color sel thistle
> color sel dark olive green
> color sel dark slate gray
> color sel wheat
> color sel linen
> color sel ghost white
> color sel rosy brown
> color sel tan
> color sel dark sea green
> color sel spring green
> color sel deep sky blue
> color sel royal blue
> color sel teal
> color sel medium turquoise
> color sel cornflower blue
> color sel orange
> color sel maroon
> color sel fire brick
> color sel dark gray
> select clear
> save "/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/dimer_apo_proteinOnly.png" width 1152 height 765
> supersample 3 transparentBackground true
> hide #4 models
> show #5 models
> view
> select #5
489 atoms, 496 bonds, 31 residues, 1 model selected
> color sel light sea green
> ui tool show "Color Actions"
> color sel dark orchid
> color sel light sea green
> color sel dark cyan
> color sel medium aquamarine
> color sel dark cyan
> color sel turquoise
> color sel dodger blue
> color sel medium spring green
> color sel dark turquoise
> color sel deep sky blue
> color sel olive drab
> color sel medium sea green
> color sel dark blue
> color sel navy
> color sel indigo
> color sel royal blue
> color sel cadet blue
> color sel steel blue
> color sel dark cyan
> color sel medium aquamarine
> color sel medium orchid
> view
> save "/Users/brittmp/OneDrive - National Institutes of Health/Ecoli
> MgtA/General Figures/MgtS.png" width 1152 height 765 supersample 3
> transparentBackground true
===== Log before crash end =====
Log:
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/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model1.pdb"
Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model1.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 7
Duplicate atom serial number found: 13
Duplicate atom serial number found: 20
94 messages similar to the above omitted
Chain information for model1.pdb #1
---
Chain | Description
L | No description available
P | No description available
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model2.pdb"
Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model2.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 7
Duplicate atom serial number found: 13
Duplicate atom serial number found: 20
94 messages similar to the above omitted
Chain information for model2.pdb #2
---
Chain | Description
L | No description available
P | No description available
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model3.pdb"
Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model3.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 7
Duplicate atom serial number found: 13
Duplicate atom serial number found: 20
94 messages similar to the above omitted
Chain information for model3.pdb #3
---
Chain | Description
L | No description available
P | No description available
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model4.pdb"
Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model4.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 7
Duplicate atom serial number found: 13
Duplicate atom serial number found: 20
94 messages similar to the above omitted
Chain information for model4.pdb #4
---
Chain | Description
L | No description available
P | No description available
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model5.pdb"
Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model5.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 7
Duplicate atom serial number found: 13
Duplicate atom serial number found: 20
94 messages similar to the above omitted
Chain information for model5.pdb #5
---
Chain | Description
L | No description available
P | No description available
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model6.pdb"
Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model6.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 7
Duplicate atom serial number found: 13
Duplicate atom serial number found: 20
94 messages similar to the above omitted
Chain information for model6.pdb #6
---
Chain | Description
L | No description available
P | No description available
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model7.pdb"
Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model7.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 7
Duplicate atom serial number found: 13
Duplicate atom serial number found: 20
94 messages similar to the above omitted
Chain information for model7.pdb #7
---
Chain | Description
L | No description available
P | No description available
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model8.pdb"
Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model8.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 7
Duplicate atom serial number found: 13
Duplicate atom serial number found: 20
94 messages similar to the above omitted
Chain information for model8.pdb #8
---
Chain | Description
L | No description available
P | No description available
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model9.pdb"
Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model9.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 7
Duplicate atom serial number found: 13
Duplicate atom serial number found: 20
94 messages similar to the above omitted
Chain information for model9.pdb #9
---
Chain | Description
L | No description available
P | No description available
> open "/Users/brittmp/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
> Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
> Results/4KYT_default_dppc_atomistic_control_OPM/model10.pdb"
Summary of feedback from opening /Users/brittmp/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Ecoli MgtA/PDBs/For Docking/SERCA Control
Molecules/4KYT_SERCA_PLN/CHARM-GUI Processed/Mem-LZerD
Results/4KYT_default_dppc_atomistic_control_OPM/model10.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 5
Duplicate atom serial number found: 7
Duplicate atom serial number found: 13
Duplicate atom serial number found: 20
94 messages similar to the above omitted
Chain information for model10.pdb #10
---
Chain | Description
L | No description available
P | No description available
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
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: MacBookPro18,2
Model Number: Z14X000HRLL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 8422.141.2.700.1
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.6.7 (22G720)
Kernel Version: Darwin 22.6.0
Time since boot: 17 days, 1 hour, 5 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2424H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 120.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
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: 2.12.1
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: 1.8
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-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: 2.1.3
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: 2.7.5
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
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: 1.16.5
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: 1.39.1
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: 2.31.0
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 , 15 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash waking Mac up from sleep |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Mac Qt 6.6 bug, crash in _NSViewHierarchyDidChangeBackingProperties. Probably wake from sleep or disconnecting or connecting external display. Have not yet seen this in Qt 6.7 in daily build.