![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15760 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-14.1-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 0x00000001e2db9ec0 (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, openmm._openmm, openmm.app.internal.compiled, 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.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._webp (total: 66)
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{
"uptime" : 150000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 4393,
"osVersion" : {
"train" : "macOS 14.1",
"build" : "23B74",
"releaseType" : "User"
},
"captureTime" : "2024-08-13 15:11:49.2148 -0400",
"codeSigningMonitor" : 1,
"incident" : "EFB1616F-F637-4038-B3E6-6B72BD52BE7B",
"pid" : 19620,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-12 18:37:07.9729 -0400",
"procStartAbsTime" : 3168971316022,
"procExitAbsTime" : 3681925374739,
"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":"BCFC189E-F43E-5EBE-9E96-04E464046690","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "99BD7651-6EDA-2D82-7078-BC72DBC083D3",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "12F3D603-8258-41C8-A4F6-218B48EB152A",
"sip" : "enabled",
"vmRegionInfo" : "0x613bd5ee5978 is not in any region. Bytes after previous region: 1355966994809 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000e13bd5ee5978","rawCodes":[1,247647108487544],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000e13bd5ee5978 -> 0x0000613bd5ee5978 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":19620},
"vmregioninfo" : "0x613bd5ee5978 is not in any region. Bytes after previous region: 1355966994809 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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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.
> open /Users/hannesludewig/Desktop/ANC2_AflAdk_MgADP_AF3_V4M_comparison.cxs
Log from Fri Aug 9 11:08:10 2024
> graphics silhouettes true
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> color name goldHL #cc9900
Color 'goldHL' is opaque: rgb(80%, 60%, 0%) hex: #cc9900
> color name lightblueHL #66ccff
Color 'lightblueHL' is opaque: rgb(40%, 80%, 100%) hex: #66ccff
> color name greenHL #009966
Color 'greenHL' is opaque: rgb(0%, 60%, 40%) hex: #009966
> color name yellowHL #cccc33
Color 'yellowHL' is opaque: rgb(80%, 80%, 20%) hex: #cccc33
> color name blueHL #006699
Color 'blueHL' is opaque: rgb(0%, 40%, 60%) hex: #006699
> color name orangeHL #cc6600
Color 'orangeHL' is opaque: rgb(80%, 40%, 0%) hex: #cc6600
> color name pinkHL #cc6699
Color 'pinkHL' is opaque: rgb(80%, 40%, 60%) hex: #cc6699
> color name darkblueHL #003478
Color 'darkblueHL' is opaque: rgb(0%, 20.4%, 47.1%) hex: #003478
> color name blueGRC #93A9D7
Color 'blueGRC' is opaque: rgb(57.6%, 66.3%, 84.3%) hex: #93a9d7
> color name lightblueGRC #DBE2F1
Color 'lightblueGRC' is opaque: rgb(85.9%, 88.6%, 94.5%) hex: #dbe2f1
> color name orangeGRC #EAB48A
Color 'orangeGRC' is opaque: rgb(91.8%, 70.6%, 54.1%) hex: #eab48a
> color name lightorangeGRC #F7E6D7
Color 'lightorangeGRC' is opaque: rgb(96.9%, 90.2%, 84.3%) hex: #f7e6d7
> color name greenGRC #B0CF94
Color 'greenGRC' is opaque: rgb(69%, 81.2%, 58%) hex: #b0cf94
> color name lightgreenGRC #E4EFDB
Color 'lightgreenGRC' is opaque: rgb(89.4%, 93.7%, 85.9%) hex: #e4efdb
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/hannesludewig/Downloads/ANC2/wt_MgADP/fold_2024_05_09_20_49_model_0.cif
Chain information for fold_2024_05_09_20_49_model_0.cif #1
---
Chain | Description
A | .
> open
> /Users/hannesludewig/Downloads/AF/AF_wt_MgADP/fold_2024_05_09_20_53_model_0.cif
Chain information for fold_2024_05_09_20_53_model_0.cif #2
---
Chain | Description
A | .
> mmaker #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 fold_2024_05_09_20_49_model_0.cif, chain A (#1) with
fold_2024_05_09_20_53_model_0.cif, chain A (#2), sequence alignment score =
891.7
RMSD between 204 pruned atom pairs is 0.799 angstroms; (across all 217 pairs:
2.301)
> lighting soft
> hide atoms
> select ::name="ADP"
108 atoms, 116 bonds, 4 residues, 2 models selected
> show sel atoms
> select ::name="MG"
2 atoms, 2 residues, 2 models selected
> show sel atoms
> select clear
> select :4
15 atoms, 13 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
> color #1 #006699ff
> color #2 #cc6600ff
> color byhetero
> select #2
1735 atoms, 1760 bonds, 220 residues, 1 model selected
> color sel goldHL
> color sel byhetero
> select clear
> select :28-31
62 atoms, 62 bonds, 8 residues, 2 models selected
> color sel light grey
> select :42-51
141 atoms, 139 bonds, 20 residues, 2 models selected
> color sel light grey
> select :58-63
92 atoms, 92 bonds, 12 residues, 2 models selected
> color sel light grey
> select :71-80
154 atoms, 153 bonds, 20 residues, 2 models selected
> color sel light grey
> select :114-120
115 atoms, 114 bonds, 14 residues, 2 models selected
> color sel light grey
> select :123-125
52 atoms, 50 bonds, 6 residues, 2 models selected
> color sel light grey
> select :161-165
77 atoms, 75 bonds, 10 residues, 2 models selected
> color sel light grey
> select :176-182
112 atoms, 112 bonds, 14 residues, 2 models selected
> color sel light grey
> select clear
> select #2/A:4@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> contacts sel restrict #2 select true reveal true
12 contacts
> select up
72 atoms, 68 bonds, 9 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> undo
> color sel orangeHL
> color sel byhetero
> select #2/A:4@CG2
1 atom, 1 residue, 1 model selected
> undo
> style sel sphere
Changed 72 atom styles
> style sel stick
Changed 72 atom styles
> hide #1 models
> select #2/A:83@CD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #2 select true reveal true
13 contacts
> select #2/A:86@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> contacts sel restrict #2 select true reveal true
26 contacts
> select #2/A:6@SD
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
39 atoms, 38 bonds, 5 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #2 select true reveal true
16 contacts
> select clear
> select #2:166
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:83@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:6@CE
1 atom, 1 residue, 1 model selected
> save /Users/hannesludewig/Desktop/ANC2_AflAdk_MgADP_AF3_V4M_comparison.cxs
——— End of log from Fri Aug 9 11:08:10 2024 ———
opened ChimeraX session
> select #2/A:4@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel ball
Changed 7 atom styles
> select clear
> select #2/A:6@CE
1 atom, 1 residue, 1 model selected
> select #2/A:182@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #2 select true
16 contacts
> select clear
> select #2/A:186@CG
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:112@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:183@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:111@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:110@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:30
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:29@CD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #2 select true
13 contacts
> select #2/A:81@CZ
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:29@CD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #2 select true
13 contacts
> select #2/A:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:107@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:5
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
39 atoms, 38 bonds, 5 residues, 1 model selected
> select clear
> select #2/A:107@CG2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #2/A:31@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> contacts sel restrict #2 select true
12 contacts
> select clear
> select #2/A:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:29@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel ball
Changed 8 atom styles
> select clear
> select #2/A:31@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
85 atoms, 85 bonds, 11 residues, 1 model selected
> style sel ball
Changed 85 atom styles
> select #2/A:182@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel ball
Changed 8 atom styles
> select clear
> hide #2.1 models
> select #2/A:64
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #2/A:68
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> ui tool show "Side View"
> select #2/A:13@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save
> /Users/hannesludewig/Desktop/ANC2_AflAdk_MgADP_AF3_V4M_comparison_cut_Afl.cxs
> hide #!2 models
> show #1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel ball
Changed 8 atom styles
> select clear
> select #1/A:4@CG1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 5 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #1 select true
14 contacts
> contacts sel restrict #1 select true reveal true
30 contacts
> select up
114 atoms, 106 bonds, 14 residues, 1 model selected
> color sel lightblueHL
> color sel byhetero
> select clear
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> select #1/A:4@CD1
1 atom, 1 residue, 1 model selected
> hide #!1 models
> show #!2 models
> open
> /Users/hannesludewig/Downloads/AF_AF3/AFwt_V4M_MgADP_AF3/fold_2024_08_09_08_30_model_0.cif
Chain information for fold_2024_08_09_08_30_model_0.cif #3
---
Chain | Description
A | .
> mmaker #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 fold_2024_05_09_20_49_model_0.cif, chain A (#1) with
fold_2024_08_09_08_30_model_0.cif, chain A (#3), sequence alignment score =
893.3
RMSD between 204 pruned atom pairs is 0.746 angstroms; (across all 217 pairs:
2.228)
> hide #!2 models
> select #3/A:5
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:4@CE
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #3 reveal true select true
17 contacts
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> select #1/A:4@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #1 reveal true select true
14 contacts
> select up
82 atoms, 77 bonds, 10 residues, 1 model selected
> contacts sel restrict #1 reveal true select true
109 contacts
> hide #1.1 models
> select clear
> select #1/A:182@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel ball
Changed 8 atom styles
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> style sel ball
Changed 2 atom styles
> select clear
> select #1/A:4@CG1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #1 reveal true select true
14 contacts
> select up
82 atoms, 77 bonds, 10 residues, 1 model selected
> contacts sel restrict #1 reveal true select true
109 contacts
> select up
301 atoms, 286 bonds, 36 residues, 1 model selected
> hide sel atoms
> select #1/A:5
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #1 reveal true select true
14 contacts
> select up
82 atoms, 77 bonds, 10 residues, 1 model selected
> select #1/A:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show sel atoms
> style sel ball
Changed 8 atom styles
> show #!2 models
> hide #!2 models
> select #1/A:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/A:29@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #1 reveal true select true
13 contacts
> select clear
> undo
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/A:72@CD2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:28@CB
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:29@CD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #1 select true
13 contacts
> select #1/A:182@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict #1 select true
26 contacts
> select clear
> select #1/A:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel blueHL
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:110@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:107@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save /Users/hannesludewig/Desktop/ANC2_AflAdk_X4M_hinge_network.cxs
> save /Users/hannesludewig/Desktop/ANC2_X4M_hinge_network.tif width 2000
> height 1265 supersample 4 transparentBackground true
> show #!2 models
> hide #!1 models
> save /Users/hannesludewig/Desktop/AflAdk_X4M_hinge_network.tif width 2000
> height 1265 supersample 4 transparentBackground true
> show #!1 models
> hide #!2 models
> save /Users/hannesludewig/Desktop/ANC2_X4M_hinge_network_normal_pose.tif
> width 2000 height 1265 supersample 4 transparentBackground true
> show #!2 models
> hide #!1 models
> save /Users/hannesludewig/Desktop/AflAdk_X4M_hinge_network_normal_pose.tif
> width 2000 height 1265 supersample 4 transparentBackground true
> hide #!2 models
> show #!1 models
> rename
Missing or invalid "models" argument: empty atom specifier
> rename #1 ANC2_WT_MgADP
> rename #1 AF3_ANC2-MgADP
> rename #2 AF3_AflAdk-MgADP
> show #!3 models
> hide #!1 models
> rename #3 AF3_ANC2:I4M-MgADP
> open
> /Users/hannesludewig/Downloads/AF_AF3/AFwt_V4M_MgADP_AF3/fold_2024_08_09_08_30_model_0.cif
Chain information for fold_2024_08_09_08_30_model_0.cif #4
---
Chain | Description
A | .
> rename #4 AF3_AflAdk:V4M-MgADP
> mmaker #4 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 AF3_ANC2-MgADP, chain A (#1) with AF3_AflAdk:V4M-MgADP, chain A
(#4), sequence alignment score = 893.3
RMSD between 204 pruned atom pairs is 0.746 angstroms; (across all 217 pairs:
2.228)
> hide #!3 models
> show #!1 models
> hide #4 models
> color #3 #006699ff
> color #4 orangeHL
> color #4 goldHL
> select #4
1736 atoms, 1761 bonds, 220 residues, 1 model selected
> colorsel
Unknown command: colorsel
> select
6950 atoms, 7051 bonds, 55 pseudobonds, 880 residues, 7 models selected
> color sel byhetero
> select clear
> show #4 models
> hide #4 models
> show #!3 models
> hide #3.1 models
> show #4 models
> hide #4 models
> hide #!3 models
> hide #!1 models
> select #3:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel light grey
> select #4:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel light grey
> select #3:42-51
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel light grey
> select #4:42-51
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel light grey
> select #3:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel light grey
> select #4:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel light grey
> select #3:71-80
77 atoms, 76 bonds, 10 residues, 1 model selected
> color sel light grey
> select #4:71-80
77 atoms, 76 bonds, 10 residues, 1 model selected
> color sel light grey
> select #3:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel light grey
> select #4:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel light grey
> select #3:123-125
26 atoms, 25 bonds, 3 residues, 1 model selected
> color sel light grey
> select #4:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel light grey
> select #3:161-165
38 atoms, 37 bonds, 5 residues, 1 model selected
> color sel light grey
> select #4:161-165
38 atoms, 37 bonds, 5 residues, 1 model selected
> color sel light grey
> select #3:176-182
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel light grey
> select #4:176-182
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel light grey
> show #!3 models
> show #4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select clear
> show #!2 models
> hide #4 models
> open "/Users/hannesludewig/Downloads/ANC2
> 2/wt_MgADP/fold_2024_05_09_20_49_model_0.cif"
Chain information for fold_2024_05_09_20_49_model_0.cif #5
---
Chain | Description
A | .
> rename #5 AF3_ANC2-MgADP_sel_winners
> color #5 lightgrey
> hide #!2 models
> select clear
> open "/Users/hannesludewig/Downloads/AF
> 2/AF_wt_MgADP/fold_2024_05_09_20_53_model_0.cif"
Chain information for fold_2024_05_09_20_53_model_0.cif #6
---
Chain | Description
A | .
> mmaker #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 AF3_ANC2-MgADP, chain A (#1) with AF3_ANC2-MgADP_sel_winners, chain
A (#5), sequence alignment score = 1130.2
RMSD between 217 pruned atom pairs is 0.000 angstroms; (across all 217 pairs:
0.000)
> mmaker #6 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 AF3_ANC2-MgADP, chain A (#1) with
fold_2024_05_09_20_53_model_0.cif, chain A (#6), sequence alignment score =
891.7
RMSD between 204 pruned atom pairs is 0.799 angstroms; (across all 217 pairs:
2.301)
> select
10428 atoms, 10580 bonds, 55 pseudobonds, 1320 residues, 9 models selected
> color sel byhetero
> select clear
> hide #6 models
> select #3:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel blueHL
> select #4:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel goldHL
> select #3:42-51
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel blueHL
> select #4:42-51
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel goldHL
> select #3:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel blueHL
> select #4:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel goldHL
> select #3:71-80
77 atoms, 76 bonds, 10 residues, 1 model selected
> color sel blueHL
> select #4:71-80
77 atoms, 76 bonds, 10 residues, 1 model selected
> color sel goldHL
> select #3:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel blueHL
> select #4:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel goldHL
> select #3:123-125
26 atoms, 25 bonds, 3 residues, 1 model selected
> color sel lblueHL
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #4:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel goldHL
> select #3:161-165
38 atoms, 37 bonds, 5 residues, 1 model selected
> color sel lblueHL
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #4:161-165
38 atoms, 37 bonds, 5 residues, 1 model selected
> color sel goldHL
> select #3:176-182
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel blueHL
> select #4:176-182
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel goldHL
> select clear
> select #3:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel light grey
> select #4:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel light grey
> select #3:42-51
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel light grey
> select #4:42-51
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel light grey
> select #3:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel light grey
> select #4:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel light grey
> select #3:71-80
77 atoms, 76 bonds, 10 residues, 1 model selected
> color sel light grey
> select #4:71-80
77 atoms, 76 bonds, 10 residues, 1 model selected
> color sel light grey
> select #3:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel light grey
> select #4:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel light grey
> select #3:123-125
26 atoms, 25 bonds, 3 residues, 1 model selected
> color sel light grey
> select #4:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel light grey
> select #3:161-165
38 atoms, 37 bonds, 5 residues, 1 model selected
> color sel light grey
> select #4:161-165
38 atoms, 37 bonds, 5 residues, 1 model selected
> color sel light grey
> select #3:176-182
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel light grey
> select #4:176-182
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel light grey
> select clear
> select #5:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel light grey
> select #6:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel light grey
> select #5:42-51
72 atoms, 71 bonds, 10 residues, 1 model selected
> color sel light grey
> select #6:42-51
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel light grey
> select #5:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel light grey
> select #6:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel light grey
> select #5:71-80
77 atoms, 77 bonds, 10 residues, 1 model selected
> color sel light grey
> select #6:71-80
77 atoms, 76 bonds, 10 residues, 1 model selected
> color sel light grey
> select #5:114-120
60 atoms, 60 bonds, 7 residues, 1 model selected
> color sel light grey
> select #6:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel light grey
> select #5:123-125
26 atoms, 25 bonds, 3 residues, 1 model selected
> color sel light grey
> select #6:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel light grey
> select #5:161-165
39 atoms, 38 bonds, 5 residues, 1 model selected
> color sel light grey
> select #6:161-165
38 atoms, 37 bonds, 5 residues, 1 model selected
> color sel light grey
> select #5:176-182
57 atoms, 57 bonds, 7 residues, 1 model selected
> color sel light grey
> select #6:176-182
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel light grey
> select clear
> select #5:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel light grey
> select #6:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel light grey
> select #5:42-51
72 atoms, 71 bonds, 10 residues, 1 model selected
> color sel light grey
> select #6:42-51
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel light grey
> select #5:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel light grey
> select #6:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel light grey
> select #5:71-80
77 atoms, 77 bonds, 10 residues, 1 model selected
> color sel light grey
> select #6:71-80
77 atoms, 76 bonds, 10 residues, 1 model selected
> color sel light grey
> select #5:114-120
60 atoms, 60 bonds, 7 residues, 1 model selected
> color sel light grey
> select #6:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel light grey
> select #5:123-125
26 atoms, 25 bonds, 3 residues, 1 model selected
> color sel light grey
> select #6:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel light grey
> select #5:161-165
39 atoms, 38 bonds, 5 residues, 1 model selected
> color sel light grey
> select #6:161-165
38 atoms, 37 bonds, 5 residues, 1 model selected
> color sel light grey
> select #5:176-182
57 atoms, 57 bonds, 7 residues, 1 model selected
> color sel light grey
> select #6:176-182
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel light grey
> select clear
> select #5:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel blueHL
> select #6:28-32
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel goldHL
> select #5:42-51
72 atoms, 71 bonds, 10 residues, 1 model selected
> color sel blueHL
> select #6:42-51
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel goldHL
> select #5:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel blueHL
> select #6:58-63
46 atoms, 46 bonds, 6 residues, 1 model selected
> color sel goldHL
> select #5:71-80
77 atoms, 77 bonds, 10 residues, 1 model selected
> color sel blueHL
> select #6:71-80
77 atoms, 76 bonds, 10 residues, 1 model selected
> color sel goldHL
> select #5:114-120
60 atoms, 60 bonds, 7 residues, 1 model selected
> color sel blueHL
> select #6:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel goldHL
> select #5:123-125
26 atoms, 25 bonds, 3 residues, 1 model selected
> color sel blueHL
> select #6:114-120
55 atoms, 54 bonds, 7 residues, 1 model selected
> color sel goldHL
> select #5:161-165
39 atoms, 38 bonds, 5 residues, 1 model selected
> color sel blueHL
> select #6:161-165
38 atoms, 37 bonds, 5 residues, 1 model selected
> color sel goldHL
> select #5:176-182
57 atoms, 57 bonds, 7 residues, 1 model selected
> color sel blueHL
> select #6:176-182
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel goldHL
> select clear
> show #6 models
> hide #6 models
> hide #5 models
> show #5 models
> cartoon suppressBackboneDisplay false
> select #5:4@ca
1 atom, 1 residue, 1 model selected
> show sel balls
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> color sel red
> select #5:4@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> select #5:4@ca
1 atom, 1 residue, 1 model selected
> color sel red
> hide sel atoms
> select clear
> hide #5 atoms
> select clear
> select #5/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel light grey
> select clear
> select ::name="ADP"
324 atoms, 348 bonds, 12 residues, 6 models selected
> show sel & #5 atoms
> select clear
> select #5:203@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel red
> select #5:203@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel darkblueHL.
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel darkblueHL
> cartoon suppressBackboneDisplay false
> select #5:203@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel darkblueHL
> select #5:166@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel blueHL
> select #5:4@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel lightblueHL
> select #5:6@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel lightblueHL
> select #5:23@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel purple
> select #5:79@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel purple
> select #6:4@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel orangeHL
> show #6 models
> hide #5 models
> select add #5
1744 atoms, 1769 bonds, 221 residues, 2 models selected
> select subtract #5
1 atom, 1 residue, 1 model selected
> hide #6 models
> select add #6
1735 atoms, 1760 bonds, 220 residues, 1 model selected
> show #6 models
> hide sel atoms
> select clear
> select ::name="ADP"
324 atoms, 348 bonds, 12 residues, 6 models selected
> show sel & #6 atoms
> select ::name="MG"
6 atoms, 6 residues, 6 models selected
> show sel & #6 atoms
> select clear
> select #6:4@ca
1 atom, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 1 atom style
> color sel orangeHL
> select clear
> show #5 models
> hide #6 models
> select #5/A:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> open 3gmt
Summary of feedback from opening 3gmt fetched from pdb
---
note | Fetching compressed mmCIF 3gmt from http://files.rcsb.org/download/3gmt.cif
3gmt title:
Crystal structure of adenylate kinase from burkholderia pseudomallei [more
info...]
Chain information for 3gmt #7
---
Chain | Description | UniProt
A B | Adenylate kinase | KAD_BURP1 1-215
Non-standard residues in 3gmt #7
---
SO4 — sulfate ion
3gmt mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> mmaker #7 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 AF3_ANC2-MgADP, chain A (#1) with 3gmt, chain B (#7), sequence
alignment score = 658.1
RMSD between 77 pruned atom pairs is 1.109 angstroms; (across all 192 pairs:
10.358)
> hide #5 models
> show #!1 models
> select clear
> hide #!1 models
> select add #7
3320 atoms, 3157 bonds, 1 pseudobond, 623 residues, 2 models selected
> rainbow sel
> select #7/A
1706 atoms, 1601 bonds, 338 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> select #7
3320 atoms, 3157 bonds, 1 pseudobond, 623 residues, 2 models selected
> hide sel atoms
> select clear
> show #!1 models
> select #7
3320 atoms, 3157 bonds, 1 pseudobond, 623 residues, 2 models selected
> color sel light grey
> select clear
> select #7:28-32
68 atoms, 66 bonds, 10 residues, 1 model selected
> color sel blueHL
> select #7:28-32
68 atoms, 66 bonds, 10 residues, 1 model selected
> color sel goldHL
> select #7:42-51
134 atoms, 134 bonds, 20 residues, 1 model selected
> color sel blueHL
> select #7:42-51
134 atoms, 134 bonds, 20 residues, 1 model selected
> color sel goldHL
> select #7:58-63
88 atoms, 88 bonds, 12 residues, 1 model selected
> color sel blueHL
> select #7:58-63
88 atoms, 88 bonds, 12 residues, 1 model selected
> color sel goldHL
> select #7:71-80
146 atoms, 144 bonds, 20 residues, 1 model selected
> color sel blueHL
> select #7:71-80
146 atoms, 144 bonds, 20 residues, 1 model selected
> color sel goldHL
> select #7:114-120
118 atoms, 116 bonds, 14 residues, 1 model selected
> color sel blueHL
> select #7:114-120
118 atoms, 116 bonds, 14 residues, 1 model selected
> color sel goldHL
> select #7:123-125
58 atoms, 56 bonds, 6 residues, 1 model selected
> color sel blueHL
> select #7:114-120
118 atoms, 116 bonds, 14 residues, 1 model selected
> color sel goldHL
> select #7:161-165
82 atoms, 80 bonds, 10 residues, 1 model selected
> color sel blueHL
> select #7:161-165
82 atoms, 80 bonds, 10 residues, 1 model selected
> color sel goldHL
> select #7:176-182
122 atoms, 126 bonds, 14 residues, 1 model selected
> color sel blueHL
> select #7:176-182
122 atoms, 126 bonds, 14 residues, 1 model selected
> color sel goldHL
> select clear
> show #6 models
> hide #!1 models
> hide #6 models
> show #5 models
> hide #!7 models
> show #6 models
> hide #5 models
> save
> /Users/hannesludewig/Desktop/Fig2_ANC2_AflAdk_sel_winner_hinges_plot.cxs
> save /Users/hannesludewig/Desktop/Fig2_AflAdk_sel_winner_hinges_plot.tif
> width 2000 height 1265 supersample 4 transparentBackground true
> show #!7 models
> hide #6 models
> show #6 models
> hide #6 models
> select #7/B:123
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
29 atoms, 28 bonds, 3 residues, 1 model selected
> color sel lightgrey
> select clear
> hide #!7 models
> show #6 models
> show #5 models
> hide #5 models
> save /Users/hannesludewig/Desktop/Fig2_AflAdk_sel_winner_hinges_plot.tif
> width 2000 height 1265 supersample 4 transparentBackground true
> show #5 models
> hide #6 models
> save /Users/hannesludewig/Desktop/Fig2_ANC2_sel_winner_hinges_plot.tif width
> 2000 height 1265 supersample 4 transparentBackground true
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #6 models
> hide #5 models
> select :157:213
88 atoms, 74 bonds, 14 residues, 7 models selected
> select #6:157:213
12 atoms, 10 bonds, 2 residues, 1 model selected
> select ~sel & ##selected
1723 atoms, 1750 bonds, 218 residues, 1 model selected
> select ~sel & ##selected
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #6:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> hide #6 models
> show #!1 models
> show #!2 models
> select #1:123
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!7 models
> show #6 models
> hide #!1 models
> show #!2 models
> show #4 models
> hide #6 models
> hide #!7 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #4 models
> show #!2 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!2 models
> select #4/A:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> hide #4 models
> hide #!2 models
> show #6 models
> show #5 models
> hide #6 models
> select #6:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #6 models
> hide #5 models
> select #6/A:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6:135
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sela toms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel atoms
> contacts sel restrict #6 reveal true select true
9 contacts
===== Log before crash end =====
Log:
> graphics silhouettes true
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> color name goldHL #cc9900
Color 'goldHL' is opaque: rgb(80%, 60%, 0%) hex: #cc9900
> color name lightblueHL #66ccff
Color 'lightblueHL' is opaque: rgb(40%, 80%, 100%) hex: #66ccff
> color name greenHL #009966
Color 'greenHL' is opaque: rgb(0%, 60%, 40%) hex: #009966
> color name yellowHL #cccc33
Color 'yellowHL' is opaque: rgb(80%, 80%, 20%) hex: #cccc33
> color name blueHL #006699
Color 'blueHL' is opaque: rgb(0%, 40%, 60%) hex: #006699
> color name orangeHL #cc6600
Color 'orangeHL' is opaque: rgb(80%, 40%, 0%) hex: #cc6600
> color name pinkHL #cc6699
Color 'pinkHL' is opaque: rgb(80%, 40%, 60%) hex: #cc6699
> color name darkblueHL #003478
Color 'darkblueHL' is opaque: rgb(0%, 20.4%, 47.1%) hex: #003478
> color name blueGRC #93A9D7
Color 'blueGRC' is opaque: rgb(57.6%, 66.3%, 84.3%) hex: #93a9d7
> color name lightblueGRC #DBE2F1
Color 'lightblueGRC' is opaque: rgb(85.9%, 88.6%, 94.5%) hex: #dbe2f1
> color name orangeGRC #EAB48A
Color 'orangeGRC' is opaque: rgb(91.8%, 70.6%, 54.1%) hex: #eab48a
> color name lightorangeGRC #F7E6D7
Color 'lightorangeGRC' is opaque: rgb(96.9%, 90.2%, 84.3%) hex: #f7e6d7
> color name greenGRC #B0CF94
Color 'greenGRC' is opaque: rgb(69%, 81.2%, 58%) hex: #b0cf94
> color name lightgreenGRC #E4EFDB
Color 'lightgreenGRC' is opaque: rgb(89.4%, 93.7%, 85.9%) hex: #e4efdb
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 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: Mac14,5
Model Number: Z17J00164LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 96 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 52 minutes, 21 seconds
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:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
R240HY:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
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: 2.12.7
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-Clipper: 0.23.0
ChimeraX-clix: 0.1.5
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-ISOLDE: 1.8.dev0
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-PhenixUI: 1.3.2
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
MolecularDynamicsViewer: 1.4
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
Send2Trash: 1.8.2
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 on Mac waking from sleep |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
ChimeraX crashed in the Qt window toolkit in native macOS call _NSViewHierarchyDidChangeBackingProperties. We've seen this dozens of times and believe it is a bug in Mac Qt 6.6. It seems to happen either when plugging in or unplugging an external display or when the Mac wakes from sleep. We have not observed the bug in Qt 6.7 which is being used in the ChimeraX daily builds. You may want to try the ChimeraX daily build.
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Reported by Hannes Ludewig