![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17330 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-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9rc202411230619 (2024-11-23 06:19:23 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 0x0000000209828840 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9-rc2024.11.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9-rc2024.11.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, _pyKVFinder, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, fontTools.misc.bezierTools, lxml._elementpath, lxml.etree, fontTools.varLib.iup, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 59)
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{
"uptime" : 29000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "Mac14,13",
"coalitionID" : 1564,
"osVersion" : {
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"build" : "24D81",
"releaseType" : "User"
},
"captureTime" : "2025-04-03 16:06:24.7067 -0400",
"codeSigningMonitor" : 1,
"incident" : "DC36E14D-41E4-475B-9A77-E989101E26C1",
"pid" : 12695,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-02 11:30:40.8720 -0400",
"procStartAbsTime" : 100317545031,
"procExitAbsTime" : 700214820746,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9-rc2024.11.23.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7965FA2B-5810-5261-BAFE-16E0353C3FB0","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "62EEF3B2-EFA4-9C30-DCBD-DC7BC6AFB635",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "6E91AC10-995E-49A9-8022-BE9A5769F600",
"sleepWakeUUID" : "0EEC425C-AECA-4EDA-A69B-DA9C673FD9A6",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x00000c0b4a76e948","rawCodes":[1,13242633480520],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000c0b4a76e948"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":12695},
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/mmitch92/Downloads/fold_slt2_hsp90_pab1_nab2/fold_slt2_hsp90_pab1_nab2_model_0.cif
Chain information for fold_slt2_hsp90_pab1_nab2_model_0.cif #1
---
Chain | Description
A | .
B C | .
D | .
E | .
> sequence chain #1/B#1/C
Alignment identifier is 1
Computing secondary structure
> select /B-C:709
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /B-C
11466 atoms, 11652 bonds, 1418 residues, 1 model selected
> ui tool show "Color Actions"
> color sel white target s
> surface sel
> transparency (#!1 & sel) 50
> color sel white target s
> hide sel cartoons
> show sel cartoons
> hide (#!1 & sel) target a
> transparency (#!1 & sel) 70
> select /A:1-484
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> ui tool show "Color Actions"
> color sel white target s
> color sel purple target s
> hide sel target a
> surface sel
> color sel purple target s
> transparency (#!1 & sel) 60
> color sel white target s
> transparency (#!1 & sel) 50
> show sel cartoons
> ui tool show "Color Actions"
> color sel purple target c
> color sel light gray target c
> color sel hot pink target c
> color sel purple target c
> set bgColor white
> color sel purple target cs
> transparency (#!1 & sel) 50
> select clear
> select
23992 atoms, 24444 bonds, 3004 residues, 1 model selected
> surface (#!1 & sel)
> transparency (#!1 & sel) 50
> show sel cartoons
> hide (#!1 & sel) target a
> ui tool show "Color Actions"
> graphics silhouettes true
> select /A:1-484
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> color sel cornflower blue target cs
> select /C
5733 atoms, 5826 bonds, 709 residues, 1 model selected
> color sel light sea green target cs
> select /B:1-709
5733 atoms, 5826 bonds, 709 residues, 1 model selected
> color sel light sea green target cs
> select /D
4082 atoms, 4171 bonds, 525 residues, 1 model selected
> color sel magenta target cs
> select /E
4528 atoms, 4617 bonds, 577 residues, 1 model selected
> color sel orange target cs
> select clear
> select /A
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> color (#!1 & sel) #fdfffbff target cs
> color (#!1 & sel) #fffaffff target cs
> color (#!1 & sel) #f6e2ffff target cs
> color (#!1 & sel) #e5bcffff target cs
> color (#!1 & sel) #d591ffff target cs
> color (#!1 & sel) #d086ffff target cs
> color (#!1 & sel) #cc7effff target cs
> color (#!1 & sel) #c874ffff target cs
> color (#!1 & sel) #c46affff target cs
> color (#!1 & sel) #c364ffff target cs
> color (#!1 & sel) #c057ffff target cs
> color (#!1 & sel) #be52ffff target cs
> color (#!1 & sel) #bc4cffff target cs
> color (#!1 & sel) #bc4bffff target cs
> color (#!1 & sel) #bb4affff target cs
> color (#!1 & sel) #ba48ffff target cs
> color (#!1 & sel) #b947ffff target cs
> color (#!1 & sel) #b543ffff target cs
> color (#!1 & sel) #af3dffff target cs
> color (#!1 & sel) #aa37ffff target cs
> color (#!1 & sel) #a835ffff target cs
> color (#!1 & sel) #a32effff target cs
> color (#!1 & sel) #9c25ffff target cs
> color (#!1 & sel) #9b21ffff target cs
> color (#!1 & sel) #9a1fffff target cs
> color (#!1 & sel) #981bffff target cs
> color (#!1 & sel) #9415ffff target cs
> color (#!1 & sel) #900cffff target cs
> color (#!1 & sel) #8d06ffff target cs
> color (#!1 & sel) #8c04ffff target cs
> color (#!1 & sel) #8a00ffff target cs
> color (#!1 & sel) #8c00ffff target cs
> color (#!1 & sel) #8900ffff target cs
> color (#!1 & sel) #8100f0ff target cs
> color (#!1 & sel) #7e00eaff target cs
> color (#!1 & sel) #7b00e5ff target cs
> color (#!1 & sel) #7800e0ff target cs
> color (#!1 & sel) #7900e1ff target cs
> color (#!1 & sel) #7c00e7ff target cs
> select
23992 atoms, 24444 bonds, 3004 residues, 1 model selected
> transparency (#!1 & sel) 50
> lighting simple
> lighting soft
> hide sel cartoons
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> select clear
> save /Users/mmitch92/Desktop/comp.png width 1729 height 881 supersample 3
> interfaces ~solvent
8 buried areas: B C 4455, E A 3942, E D 1841, C D 1683, D A 1177, B D 535, C A
446, B A 357
> show cartoons
> save "/Users/mmitch92/Desktop/comp rib.png" width 1729 height 881
> supersample 3
> color (#!1 & sel) red
> surface hidePatches (#!1 & sel)
> ui tool show "Render/Select by Attribute"
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.4
which is incompatible.
nptyping 2.5.0 requires numpy=1.20.0; python_version >= "3.8", but you
have numpy 2.2.4 which is incompatible.
\---
pip standard output:
\---
\---
> kvfinder
142 cavities found for fold_slt2_hsp90_pab1_nab2_model_0.cif #1
fold_slt2_hsp90_pab1_nab2_model_0.cif Cavities
---
ID | | Volume | Area | Points
1.6.61 | | 2123.28 | 1648.19 | 9830
1.6.2 | | 724.9 | 596.55 | 3356
1.6.29 | | 690.77 | 573.27 | 3198
1.6.31 | | 638.06 | 495.36 | 2954
1.6.92 | | 489.24 | 455.69 | 2265
1.6.111 | | 298.73 | 365.02 | 1383
1.6.59 | | 214.06 | 180.52 | 991
1.6.50 | | 196.56 | 177.69 | 910
1.6.47 | | 193.97 | 162.56 | 898
1.6.87 | | 189 | 144.39 | 875
1.6.100 | | 174.96 | 167.32 | 810
1.6.83 | | 172.15 | 195.6 | 797
1.6.7 | | 169.56 | 150.33 | 785
1.6.18 | | 163.51 | 162.09 | 757
1.6.74 | | 158.54 | 163.85 | 734
1.6.24 | | 156.17 | 171.84 | 723
1.6.73 | | 151.42 | 162.96 | 701
1.6.57 | | 147.53 | 131.8 | 683
1.6.71 | | 144.07 | 159.41 | 667
1.6.75 | | 141.05 | 140.44 | 653
1.6.55 | | 130.46 | 127.39 | 604
1.6.107 | | 128.3 | 158.94 | 594
1.6.35 | | 116.64 | 131.23 | 540
1.6.131 | | 107.14 | 133.4 | 496
1.6.15 | | 106.92 | 137.66 | 495
1.6.42 | | 99.14 | 97.85 | 459
1.6.65 | | 92.02 | 87.35 | 426
1.6.99 | | 90.5 | 64.52 | 419
1.6.33 | | 90.29 | 104.16 | 418
1.6.130 | | 87.91 | 107.95 | 407
1.6.16 | | 86.62 | 133.01 | 401
1.6.123 | | 82.94 | 115.48 | 384
1.6.9 | | 72.58 | 83.57 | 336
1.6.129 | | 68.47 | 66.16 | 317
1.6.115 | | 66.31 | 90.39 | 307
1.6.103 | | 63.29 | 52.62 | 293
1.6.23 | | 61.56 | 82.82 | 285
1.6.64 | | 58.97 | 68.16 | 273
1.6.6 | | 57.67 | 56.68 | 267
1.6.135 | | 57.46 | 66.95 | 266
1.6.72 | | 55.3 | 66.96 | 256
1.6.109 | | 54.86 | 44.84 | 254
1.6.26 | | 53.35 | 42.39 | 247
1.6.136 | | 52.49 | 54.34 | 243
1.6.60 | | 52.27 | 57.11 | 242
1.6.36 | | 47.09 | 65.76 | 218
1.6.120 | | 46.01 | 59.96 | 213
1.6.68 | | 45.58 | 45.39 | 211
1.6.125 | | 44.28 | 59.08 | 205
1.6.138 | | 43.2 | 56.17 | 200
1.6.1 | | 41.9 | 41.91 | 194
1.6.52 | | 41.47 | 42.6 | 192
1.6.22 | | 41.26 | 39.36 | 191
1.6.3 | | 40.82 | 65.38 | 189
1.6.38 | | 34.56 | 57.32 | 160
1.6.142 | | 34.56 | 43.43 | 160
1.6.113 | | 33.26 | 36.22 | 154
1.6.128 | | 33.05 | 25.09 | 153
1.6.19 | | 32.18 | 52.91 | 149
1.6.93 | | 30.67 | 47.9 | 142
1.6.97 | | 29.16 | 49.48 | 135
1.6.114 | | 29.16 | 44.39 | 135
1.6.8 | | 28.94 | 48.58 | 134
1.6.46 | | 28.94 | 53.64 | 134
1.6.84 | | 28.3 | 45.2 | 131
1.6.5 | | 28.08 | 33.08 | 130
1.6.51 | | 27.22 | 66.82 | 126
1.6.63 | | 27 | 28.85 | 125
1.6.105 | | 25.92 | 42.6 | 120
1.6.141 | | 25.92 | 48.36 | 120
1.6.25 | | 25.06 | 25.58 | 116
1.6.10 | | 24.62 | 37.83 | 114
1.6.126 | | 23.33 | 29.64 | 108
1.6.70 | | 22.9 | 41.28 | 106
1.6.106 | | 22.9 | 41.28 | 106
1.6.122 | | 22.25 | 44.42 | 103
1.6.118 | | 21.82 | 40.63 | 101
1.6.56 | | 21.17 | 39.07 | 98
1.6.79 | | 21.17 | 39.07 | 98
1.6.119 | | 21.17 | 27.72 | 98
1.6.102 | | 20.74 | 31 | 96
1.6.104 | | 20.74 | 29.14 | 96
1.6.54 | | 20.52 | 33.1 | 95
1.6.77 | | 19.87 | 36.19 | 92
1.6.12 | | 19.01 | 25.37 | 88
1.6.49 | | 19.01 | 27.06 | 88
1.6.48 | | 18.58 | 31.54 | 86
1.6.67 | | 18.14 | 23.63 | 84
1.6.20 | | 17.28 | 36.68 | 80
1.6.90 | | 17.28 | 25.53 | 80
1.6.11 | | 16.85 | 32.3 | 78
1.6.14 | | 16.85 | 32.3 | 78
1.6.40 | | 16.85 | 32.3 | 78
1.6.41 | | 16.85 | 32.3 | 78
1.6.110 | | 15.55 | 27.18 | 72
1.6.85 | | 15.34 | 22.94 | 71
1.6.30 | | 14.69 | 22.65 | 68
1.6.69 | | 14.69 | 30.01 | 68
1.6.117 | | 14.26 | 29.73 | 66
1.6.89 | | 14.04 | 25.4 | 65
1.6.88 | | 13.82 | 19.16 | 64
1.6.121 | | 12.74 | 23.58 | 59
1.6.27 | | 12.53 | 16.85 | 58
1.6.13 | | 12.31 | 29.54 | 57
1.6.21 | | 12.31 | 29.54 | 57
1.6.37 | | 12.31 | 29.54 | 57
1.6.44 | | 12.31 | 29.54 | 57
1.6.45 | | 12.31 | 29.54 | 57
1.6.78 | | 12.31 | 29.54 | 57
1.6.86 | | 12.31 | 29.54 | 57
1.6.98 | | 12.31 | 29.54 | 57
1.6.101 | | 12.31 | 29.54 | 57
1.6.108 | | 12.31 | 29.54 | 57
1.6.112 | | 12.31 | 29.54 | 57
1.6.124 | | 12.31 | 29.54 | 57
1.6.133 | | 12.31 | 29.54 | 57
1.6.53 | | 11.45 | 16.59 | 53
1.6.95 | | 11.45 | 19.42 | 53
1.6.66 | | 11.23 | 21.92 | 52
1.6.43 | | 10.37 | 17.63 | 48
1.6.81 | | 9.72 | 18.49 | 45
1.6.28 | | 9.5 | 17.33 | 44
1.6.4 | | 9.07 | 18.49 | 42
1.6.62 | | 9.07 | 14.71 | 42
1.6.80 | | 8.86 | 17.29 | 41
1.6.32 | | 8.21 | 19.51 | 38
1.6.76 | | 7.99 | 15.79 | 37
1.6.96 | | 7.78 | 15.17 | 36
1.6.127 | | 7.78 | 14.87 | 36
1.6.132 | | 7.78 | 14.94 | 36
1.6.94 | | 6.91 | 16.05 | 32
1.6.134 | | 6.91 | 15.7 | 32
1.6.17 | | 6.7 | 13.98 | 31
1.6.139 | | 6.7 | 11.27 | 31
1.6.137 | | 6.48 | 14.56 | 30
1.6.82 | | 6.05 | 9.48 | 28
1.6.116 | | 6.05 | 13.31 | 28
1.6.34 | | 5.62 | 10.83 | 26
1.6.39 | | 5.62 | 11.34 | 26
1.6.91 | | 5.4 | 10.51 | 25
1.6.58 | | 5.18 | 10.73 | 24
1.6.140 | | 5.18 | 12.26 | 24
Populating font family aliases took 146 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> undo
> ui tool show "Find Cavities"
> close session
> open
> /Users/mmitch92/Downloads/fold_slt2_hsp90_pab1_nab2/fold_slt2_hsp90_pab1_nab2_model_0.cif
> format mmcif
Chain information for fold_slt2_hsp90_pab1_nab2_model_0.cif #1
---
Chain | Description
A | .
B C | .
D | .
E | .
> select /A:1-484
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> color sel magenta
> select /C:1-709
5733 atoms, 5826 bonds, 709 residues, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> interfaces ~solvent
8 buried areas: B C 4455, E A 3942, E D 1841, C D 1683, D A 1177, B D 535, C A
446, B A 357
> select /B
5733 atoms, 5826 bonds, 709 residues, 1 model selected
> color sel orange
> select /C
5733 atoms, 5826 bonds, 709 residues, 1 model selected
> color sel orange
> select /D
4082 atoms, 4171 bonds, 525 residues, 1 model selected
> ui tool show "Color Actions"
> color sel blue violet target acspfl
> select /E
4528 atoms, 4617 bonds, 577 residues, 1 model selected
> color sel medium aquamarine target acspfl
> select /B
5733 atoms, 5826 bonds, 709 residues, 1 model selected
> hide sel target a
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> interfaces ~solvent
8 buried areas: B C 4455, E A 3942, E D 1841, C D 1683, D A 1177, B D 535, C A
446, B A 357
> select /B
5733 atoms, 5826 bonds, 709 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> interfaces ~solvent
5 buried areas: E A 3942, E D 1841, C D 1683, D A 1177, C A 446
> interfaces ~solvent
5 buried areas: E A 3942, E D 1841, C D 1683, D A 1177, C A 446
> save /Users/mmitch92/Desktop/slte.png width 1729 height 881 supersample 3
> save "/Users/mmitch92/Desktop/explode slt.png" width 1729 height 881
> supersample 3
> color sel lime target acspfl
> color sel deep pink target acspfl
> undo
> select clear
> save "/Users/mmitch92/Desktop/residue slt.png" width 1729 height 881
> supersample 3
> select ~sel & ##selected
16494 atoms, 16924 bonds, 2085 residues, 1 model selected
> hide sel target a
> hbonds sel reveal true
1673 hydrogen bonds found
> ~hbonds
> undo
Undo failed, probably because structures have been modified.
> color sel dark blue target acspfl
> color sel dark magenta target acspfl
> color sel orchid target acspfl
> color sel medium spring green target acspfl
> color sel brown target acspfl
> color sel alice blue target acspfl
> color sel medium slate blue target acspfl
> color sel dark cyan target acspfl
> color sel hot pink target acspfl
> color sel navy target acspfl
> color sel dark blue target acspfl
> color sel medium blue target acspfl
> style sel ball
Changed 1765 atom styles
> select clear
> surface
> transparency 60
> select
18259 atoms, 18618 bonds, 2295 residues, 1 model selected
> transparency (#!1 & sel) 60
> hide (#!1 & sel) target a
> style sel ball
Changed 1765 atom styles
> show (#!1 & sel) target ab
> style sel sphere
Changed 1765 atom styles
> style sel stick
Changed 1765 atom styles
> cartoon (#!1 & sel)
Computing secondary structure
> select
18259 atoms, 18618 bonds, 2295 residues, 1 model selected
> show sel cartoons
> color sel spring green target acspfl
> select ~sel & ##selected
16494 atoms, 16924 bonds, 2085 residues, 1 model selected
> transparency (#!1 & sel) 100
> transparency (#!1 & sel) 80
> cartoon hide (#!1 & sel)
> select ~sel & ##selected
1765 atoms, 1694 bonds, 210 residues, 1 model selected
> style sel sphere
Changed 1765 atom styles
> style sel ball
Changed 1765 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> color sel deep pink target acspfl
> surface hidePatches (#!1 & sel)
> select clear
> transparency 50
> save /Users/mmitch92/Desktop/interact.png width 1729 height 881 supersample
> 3
> hbonds reveal true
1727 hydrogen bonds found
> hbonds reveal true
1727 hydrogen bonds found
> hbonds reveal true
1727 hydrogen bonds found
> ui tool show Distances
> undo
> ~hbonds
> color sel spring green target acspfl
> select ~sel & ##selected
16494 atoms, 16924 bonds, 2085 residues, 1 model selected
> transparency (#!1 & sel) 80
> hide (#!1 & sel) target a
> transparency (#!1 & sel) 30
> hide sel cartoons
> transparency (#!1 & sel) 90
> transparency (#!1 & sel) 70
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> color (#!1 & sel) black
> color sel dark blue target acspfl
> color sel medium blue target acspfl
> color sel blue target acspfl
> style (#!1 & sel) ball
Changed 1765 atom styles
> select ~sel & ##selected
16494 atoms, 16924 bonds, 2085 residues, 1 model selected
> transparency (#!1 & sel) 50
> transparency (#!1 & sel) 0
> transparency (#!1 & sel) 30
> transparency (#!1 & sel) 70
> graphics silhouettes true
> select ~sel & ##selected
1765 atoms, 1694 bonds, 210 residues, 1 model selected
> color sel lime target acspfl
> color sel lime green target acspfl
> color sel chartreuse target acspfl
> color sel lime green target acspfl
> graphics silhouettes false
> graphics silhouettes true
> show (#!1 & sel) target ab
> style sel sphere
Changed 1765 atom styles
> style sel stick
Changed 1765 atom styles
> color sel medium sea green target acspfl
> color sel lawn green target acspfl
> style sel ball
Changed 1765 atom styles
> select clear
> save /Users/mmitch92/Desktop/next.png width 1729 height 881 supersample 3
> transparency 20
> show cartoons
> hide surfaces
> show surfaces
> hide atoms
> hide surfaces
> hide cartoons
> show cartoons
> show surfaces
> lighting flat
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> transparency 0
> graphics silhouettes false
> lighting shadows false
> lighting flat
> select /A
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> color (#!1 & sel) magenta
> select /C
5733 atoms, 5826 bonds, 709 residues, 1 model selected
> color (#!1 & sel) orange
> select /D
4082 atoms, 4171 bonds, 525 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium orchid target acspfl
> color sel dark violet target acspfl
> select /E
4528 atoms, 4617 bonds, 577 residues, 1 model selected
> color sel dark cyan target acspfl
> select /A
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> color sel deep pink target acspfl
> color sel pale violet red target acspfl
> select clear
> lighting flat
> graphics silhouettes false
> transparency 40
> cartoon hide
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> show cartoons
> hide atoms
> hide surfaces
> show surfaces
> show cartoons
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> lighting flat
> transparency 60
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> ui tool show "Side View"
> save "/Users/mmitch92/Desktop/comp rib.png" width 1729 height 881
> supersample 3
> interfaces ~solvent
5 buried areas: E A 3942, E D 1841, C D 1683, D A 1177, C A 446
> save /Users/mmitch92/Desktop/exploded.png width 1729 height 881 supersample
> 3
> color (#!1 & sel) black
> surface hidePatches (#!1 & sel)
> show (#!1 & sel) target ab
> style sel sphere
Changed 1765 atom styles
> color (#!1 & sel) gray
> select clear
> save /Users/mmitch92/Desktop/sele.png width 1344 height 765 supersample 3
> save "/Users/mmitch92/Desktop/sele trans.png" width 1344 height 765
> supersample 3 transparentBackground true
> select /A:1-484
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> select /A:1-484
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> select /A
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> color sel orange target acspfl
> color sel dark violet target acspfl
> select /C
5733 atoms, 5826 bonds, 709 residues, 1 model selected
> color sel cadet blue target acspfl
> select /D
4082 atoms, 4171 bonds, 525 residues, 1 model selected
> color sel hot pink target acspfl
> select /E
4528 atoms, 4617 bonds, 577 residues, 1 model selected
> color sel medium sea green target acspfl
> color sel orange target acspfl
> color sel coral target acspfl
> color sel orange target acspfl
> select clear
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting flat
> graphics silhouettes false
> lighting simple
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting flat
> lighting full
> transparency 50
> cartoon style xsection oval modeHelix default
> transparency 30
> transparency 40
> show atoms
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting shadows false
> set bgColor gray
> set bgColor #80808000
> set bgColor black
> set bgColor transparent
> transparency 60
> hide atoms
> save /Users/mmitch92/Desktop/bg.png width 1344 height 765 supersample 3
> set bgColor white
> set bgColor #ffffff00
> save /Users/mmitch92/Desktop/bgw.png width 1344 height 765 supersample 3
> save /Users/mmitch92/Desktop/exp.png width 1344 height 765 supersample 3
> select /A
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> select ~sel & ##selected
14343 atoms, 14614 bonds, 1811 residues, 1 model selected
> hide (#!1 & sel) target a
> surface hidePatches (#!1 & sel)
> cartoon hide (#!1 & sel)
> save /Users/mmitch92/Desktop/mpk1.png width 1344 height 765 supersample 3
> select ~sel & ##selected
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> surface (#!1 & sel)
> select ~sel & ##selected
14343 atoms, 14614 bonds, 1811 residues, 1 model selected
> surface (#!1 & sel)
> show (#!1 & sel) target ab
> select ~sel & ##selected
3916 atoms, 4004 bonds, 484 residues, 1 model selected
> show (#!1 & sel) target ab
> select clear
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> save /Users/mmitch92/Desktop/1.png width 1344 height 765 supersample 3
> hide (#!1 & sel) target a
> show (#!1 & sel) target ab
> select /C
5733 atoms, 5826 bonds, 709 residues, 1 model selected
> hide (#!1 & sel) target a
> surface hidePatches (#!1 & sel)
> select /D
4082 atoms, 4171 bonds, 525 residues, 1 model selected
> color (#!1 & sel) light sea green
> color sel light coral target acspfl
> color sel sky blue target acspfl
> color sel dark slate blue target acspfl
> color (#!1 & sel) #413be7ff
> color (#!1 & sel) #423be8ff
> color (#!1 & sel) #423ceaff
> color (#!1 & sel) #433deeff
> color (#!1 & sel) #443ef0ff
> color (#!1 & sel) #453ff5ff
> color (#!1 & sel) #4740faff
> color (#!1 & sel) #4740fbff
> color (#!1 & sel) #4741fdff
> color (#!1 & sel) #4841ffff
> color (#!1 & sel) #4740fcff
> color (#!1 & sel) #3a35ceff
> color (#!1 & sel) #3832c5ff
> color (#!1 & sel) #3732c2ff
> color (#!1 & sel) #3530bdff
> color (#!1 & sel) #3530bcff
> color (#!1 & sel) #3530bbff
> color (#!1 & sel) #3530baff
> color (#!1 & sel) #342fb6ff
> color (#!1 & sel) #332fb6ff
> color (#!1 & sel) #322eb2ff
> color (#!1 & sel) #312cadff
> color (#!1 & sel) #312cabff
> color (#!1 & sel) #302ba8ff
> color (#!1 & sel) #2d299eff
> color (#!1 & sel) #2c289dff
> color (#!1 & sel) #2b2799ff
> color (#!1 & sel) #2a2696ff
> color (#!1 & sel) #2a2694ff
> color (#!1 & sel) #292692ff
> color (#!1 & sel) #292590ff
> color (#!1 & sel) #28248eff
> color (#!1 & sel) #27248bff
> color (#!1 & sel) #272388ff
> color (#!1 & sel) #252284ff
> color (#!1 & sel) #252182ff
> color (#!1 & sel) #252181ff
> color (#!1 & sel) #24207fff
> color (#!1 & sel) #23207cff
> color (#!1 & sel) #221f79ff
> color (#!1 & sel) #221f78ff
> color (#!1 & sel) #1a1878ff
> color (#!1 & sel) #191878ff
> color (#!1 & sel) #171a78ff
> color (#!1 & sel) #151e78ff
> color (#!1 & sel) #122178ff
> color (#!1 & sel) #102578ff
> color (#!1 & sel) #0c2a78ff
> color (#!1 & sel) #0c2b78ff
> color (#!1 & sel) #0d2c78ff
> color (#!1 & sel) #0d2d78ff
> color (#!1 & sel) #0f2f78ff
> color (#!1 & sel) #113178ff
> color (#!1 & sel) #123278ff
> color (#!1 & sel) #123279ff
> color (#!1 & sel) #143989ff
> color (#!1 & sel) #1742a0ff
> color (#!1 & sel) #1843a3ff
> color (#!1 & sel) #1843a1ff
> color (#!1 & sel) #17409cff
> color (#!1 & sel) #163d94ff
> color (#!1 & sel) #153c93ff
> color (#!1 & sel) #204393ff
> color (#!1 & sel) #204293ff
> color (#!1 & sel) #204193ff
> color (#!1 & sel) #204093ff
> color (#!1 & sel) #213d93ff
> color (#!1 & sel) #223c93ff
> color (#!1 & sel) #223a93ff
> color (#!1 & sel) #233993ff
> color (#!1 & sel) #253593ff
> color (#!1 & sel) #263493ff
> color (#!1 & sel) #263293ff
> color (#!1 & sel) #273093ff
> color (#!1 & sel) #283093ff
> color (#!1 & sel) #282f93ff
> color (#!1 & sel) #2a2b93ff
> color (#!1 & sel) #2e2c93ff
> color (#!1 & sel) #332d93ff
> color (#!1 & sel) #382f93ff
> color (#!1 & sel) #3c3093ff
> color (#!1 & sel) #3f3193ff
> color (#!1 & sel) #443393ff
> color (#!1 & sel) #463493ff
> color (#!1 & sel) #473593ff
> color (#!1 & sel) #4b3793ff
> color (#!1 & sel) #4c3893ff
> color (#!1 & sel) #4d3893ff
> color (#!1 & sel) #4f3b93ff
> color (#!1 & sel) #503c93ff
> color (#!1 & sel) #513d93ff
> color (#!1 & sel) #533f93ff
> color (#!1 & sel) #544093ff
> color (#!1 & sel) #544193ff
> color (#!1 & sel) #554293ff
> color (#!1 & sel) #524193ff
> color (#!1 & sel) #4e3f93ff
> color (#!1 & sel) #4b3e93ff
> color (#!1 & sel) #473d93ff
> color (#!1 & sel) #473c93ff
> color (#!1 & sel) #463c93ff
> color (#!1 & sel) #433b93ff
> color (#!1 & sel) #403993ff
> color (#!1 & sel) #383593ff
> color (#!1 & sel) #363493ff
> color (#!1 & sel) #363393ff
> color (#!1 & sel) #333193ff
> color (#!1 & sel) #323193ff
> color (#!1 & sel) #313093ff
> color (#!1 & sel) #2f2f93ff
> color (#!1 & sel) #2d2d93ff
> color (#!1 & sel) #2c2d93ff
> color (#!1 & sel) #2b2c93ff
> color (#!1 & sel) #2a2c93ff
> color (#!1 & sel) #292b93ff
> color (#!1 & sel) #282a93ff
> color (#!1 & sel) #282d93ff
> color (#!1 & sel) #2a3393ff
> color (#!1 & sel) #2c3b93ff
> color (#!1 & sel) #2f4793ff
> color (#!1 & sel) #304a93ff
> color (#!1 & sel) #335093ff
> color (#!1 & sel) #355493ff
> color (#!1 & sel) #355593ff
> color (#!1 & sel) #375993ff
> color (#!1 & sel) #385c93ff
> color (#!1 & sel) #3a6093ff
> color (#!1 & sel) #3a6493ff
> color (#!1 & sel) #3a6593ff
> color (#!1 & sel) #376593ff
> color (#!1 & sel) #336593ff
> color (#!1 & sel) #2b6693ff
> color (#!1 & sel) #276793ff
> color (#!1 & sel) #266793ff
> color (#!1 & sel) #256793ff
> color (#!1 & sel) #256693ff
> color (#!1 & sel) #246493ff
> color (#!1 & sel) #236393ff
> color (#!1 & sel) #236293ff
> color (#!1 & sel) #226193ff
> color (#!1 & sel) #226093ff
> color (#!1 & sel) #215b93ff
> color (#!1 & sel) #215993ff
> select clear
> interfaces ~solvent
5 buried areas: E A 3942, E D 1841, C D 1683, D A 1177, C A 446
> interfaces ~solvent
5 buried areas: E A 3942, E D 1841, C D 1683, D A 1177, C A 446
> interfaces ~solvent
5 buried areas: E A 3942, E D 1841, C D 1683, D A 1177, C A 446
> interfaces ~solvent
5 buried areas: E A 3942, E D 1841, C D 1683, D A 1177, C A 446
> save /Users/mmitch92/Desktop/k.png width 1729 height 881 supersample 3
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,13
Model Number: Z17Z000PJLL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 96 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 6 days, 2 hours, 23 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL S3422DWG:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 100.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
DELL P2417H:
Resolution: 1080 x 1920
UI Looks like: 1080 x 1920 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 90
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9rc202411230619
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
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: 1.2.1
ChimeraX-Label: 1.1.11
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-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
ChimeraX-OrthoPick: 1.0.1
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.3.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 1.33.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.4
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 6.0.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.3
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 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 , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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