![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 7 months ago
#17231 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: 1.8 (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 0x00000001fc574840 (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.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 62)
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{
"uptime" : 320000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 21145,
"osVersion" : {
"train" : "macOS 15.3.2",
"build" : "24D81",
"releaseType" : "User"
},
"captureTime" : "2025-03-28 14:05:10.9707 -0700",
"codeSigningMonitor" : 1,
"incident" : "F33AA3F3-3BF6-4F70-B776-F01935A464ED",
"pid" : 39485,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-28 10:48:27.3204 -0700",
"procStartAbsTime" : 7570135006179,
"procExitAbsTime" : 7853421525233,
"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":"8130645D-BEAB-5776-BE53-C039A7FAE8AE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "34646E04-77D9-22C8-5CBA-A82BA218D2EA",
"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" : "0C17CBEB-30D5-476A-8EB6-962600B7C5A8",
"wakeTime" : 24437,
"sleepWakeUUID" : "3BB03096-279A-42CD-A91D-F49A1B352983",
"sip" : "enabled",
"vmRegionInfo" : "0x1ab64af36b58 is not in any region. Bytes after previous region: 28889207499609 Bytes before following region: 76182872429736\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00001ab64af36b58","rawCodes":[1,29370243836760],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00001ab64af36b58"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":39485},
"vmregioninfo" : "0x1ab64af36b58 is not in any region. Bytes after previous region: 28889207499609 Bytes before following region: 76182872429736\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.40.6"
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"arch" : "arm64e",
"base" : 6853718016,
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"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 5427200,
"uuid" : "f66e0c94-99b5-3fcd-b726-3e3cbca668a3",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
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"base" : 6755241984,
"size" : 290816,
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"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
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"base" : 6757478400,
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"size" : 5197824,
"uuid" : "190e6a36-fcaa-3ea3-94bb-7009c44653da",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
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"arch" : "arm64e",
"base" : 6947135488,
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3178496,
"uuid" : "950f1236-acaf-379d-819f-6c6b0b5deabd",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
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"uuid" : "398a133c-9bcb-317f-a064-a40d3cea3c0f",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
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/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/bft-1_project/structures/bft1_8h3y_nanbody.pdb1
Summary of feedback from opening
/Users/poojasrinivas/Library/CloudStorage/OneDrive-
UW/Desktop/mougouslab/bft-1_project/structures/bft1_8h3y_nanbody.pdb1
---
warnings | Start residue of secondary structure not found: HELIX 15 AB6 SER B 44 ASP B 54 1 11
Start residue of secondary structure not found: HELIX 16 AB7 ARG B 96 ASP B 99
5 4
Start residue of secondary structure not found: HELIX 17 AB8 GLU B 128 ALA B
141 1 14
Start residue of secondary structure not found: HELIX 18 AB9 PRO B 142 LYS B
144 5 3
Start residue of secondary structure not found: HELIX 19 AC1 ASN B 150 GLU B
153 5 4
94 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (22 )
Cannot find LINK/SSBOND residue CYS (22 )
Cannot find LINK/SSBOND residue ASP (194 )
Cannot find LINK/SSBOND residue ASP (194 )
Cannot find LINK/SSBOND residue HIS (348 )
7 messages similar to the above omitted
bft1_8h3y_nanbody.pdb1 title:
Bacteroide fragilis toxin In complex with nanobody 327 [more info...]
Chain information for bft1_8h3y_nanbody.pdb1 #1
---
Chain | Description
A | No description available
F | No description available
Non-standard residues in bft1_8h3y_nanbody.pdb1 #1
---
ZN — zinc ion
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting soft
> select /F:2-121
918 atoms, 939 bonds, 120 residues, 1 model selected
> hide sel cartoons
> hide pseudobondes
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> select :221
13 atoms, 12 bonds, 2 residues, 1 model selected
> select :211
1 atom, 1 residue, 1 model selected
> color :1-199 white
> color :199-500 purple
> color sel byhetero
> ui mousemode right select
> color sel byhetero
> select add #1
3868 atoms, 3739 bonds, 7 pseudobonds, 675 residues, 3 models selected
> color sel byhetero
> select clear
> select /A:401@ZN
1 atom, 1 residue, 1 model selected
> color sel green
> hbonds sel reveal true
0 hydrogen bonds found
> select clear
> hbonds reveal true
912 hydrogen bonds found
> ~hbonds
> hide :HOH
> hide atoms
> ui tool show "Side View"
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> graphics silhouettes true
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/prodomaincloseup.png width
> 1800 height 1800 supersample 4 transparentBackground true
> hbonds reveal true
912 hydrogen bonds found
> clip off
> ~hbonds
> hide #1
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/bft-1_project/structures/BFT_Minibinder_3.pdb
Chain information for BFT_Minibinder_3.pdb #2
---
Chain | Description
A | No description available
B | No description available
> matchmaker #2 to #`
Invalid "to" argument: invalid atoms specifier
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bft1_8h3y_nanbody.pdb1, chain A (#1) with BFT_Minibinder_3.pdb,
chain A (#2), sequence alignment score = 971.5
RMSD between 186 pruned atom pairs is 0.400 angstroms; (across all 186 pairs:
0.400)
> hide #2/A
> hide #2/A cartoons
> color #2/B #EAAE11
Drag select of 1 residues
> color sel white
> select clear
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/bft-1_project/newminibinders/fold_bft1_fold_kl_d2_3_model_0_7_b/fold_bft1_fold_kl_d2_3_model_0_7_b_model_0.cif
Chain information for fold_bft1_fold_kl_d2_3_model_0_7_b_model_0.cif #3
---
Chain | Description
A | .
B | .
> matchmaker #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 bft1_8h3y_nanbody.pdb1, chain A (#1) with
fold_bft1_fold_kl_d2_3_model_0_7_b_model_0.cif, chain B (#3), sequence
alignment score = 960.7
RMSD between 183 pruned atom pairs is 0.430 angstroms; (across all 186 pairs:
0.592)
> hide #3/B surfaces
> hide #3/B cartoons
> hide #3 models
> hide #2#!1 atoms
> transparency #1/ :1-199 target c
Missing or invalid "percent" argument: Expected a number
> transparency 100 #1/ :1-199 target c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 #1/ :1-199 target cartoons
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #1/ :1-199 100 target cartoons
Missing or invalid "percent" argument: Expected a number
> transparency #1/:1-199 100 target cartoons
Missing or invalid "percent" argument: Expected a number
> transparency #1/:1-199 100 target cartoons
Missing or invalid "percent" argument: Expected a number
> transparency #1/:1-199 100 target cartoons
Missing or invalid "percent" argument: Expected a number
> transparency #1:1-199 100 target cartoons
Invalid "target" argument: Character 't' is not an allowed target, must be one
of acrsbmpfl
> transparency #1:1-199 100 cartoons
> hide #1:1-199 cartoons
> hide #2 models
> show #2 models
> show #1:1-199 cartoons
> show #1/A:1-199 cartoons
> color #1:1-199 white
> color #1/A:1-199 white
> transparency #1:1-199 0 cartoons
Drag select of 4 residues
> show sel cartoons
> show #1 cartoons
> undo
> select clear
> show pseudobonds
Drag select of 2 residues, 1 pseudobonds
> hide sel pseudobonds
> select clear
> hide #2 models
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/fulllengthBFT_backside.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #1:1-199 cartoons
> hide pseudobonds
Drag select of 2 atoms, 1 pseudobonds
> hide sel atoms
> select #1/A:199@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!1 atoms
> show #2 models
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft_mb03_backside.png width
> 1800 height 1800 supersample 4 transparentBackground true
> show #1/A
> show #1/A cartoons
> hide #2 models
Drag select of 1 residues, 1 pseudobonds
> hide sel pseudobonds
> select clear
> show sel pseudobonds
> select clear
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/fulllengthBFT_backside2.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #1:1-199 cartoons
> hide #1:1-199 pseudobonds
> select clear
> hide #!1 atoms
> select clear
> show #2 models
> show #1:1-199 cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A :RENG
Nothing selected
> select #1/A :R,E,N,G
Nothing selected
> select #1/A @R,E,N,G
348 atoms, 348 residues, 1 model selected
> select clear
> select #1/A :Arg,Glu
302 atoms, 271 bonds, 32 residues, 1 model selected
> select #1/A :Arg,Glu,Gln,Gly
467 atoms, 412 bonds, 62 residues, 1 model selected
> select #1/A:226
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:226
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel green
> select #1/A:238
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:238
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel green
> select #1/A:246
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:246
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel green
> select #1/A:255
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:254-255
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:254-255
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:254-255
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:255
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:255
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel green
> select #1/A:262
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:262
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel green
> select #1/A:265
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:265
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel green
> select #1/A:296
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:296-297
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/A:296-297
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/A:296-297
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/A:296
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:296
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel green
> select clear
> hide #!1 models
> show #!1 models
> hide #1/F
> hide #1/F cartoons
> hide #1:1-199 cartoons
> hide #2 models
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bftcartoon_interactingresidues.png
> width 1800 height 1800 supersample 4 transparentBackground true
> select #1 :238,246,255,262,265,296
59 atoms, 55 bonds, 7 residues, 1 model selected
> select clear
> show #2 models
> select #1 :238,246,255,262,265,296
59 atoms, 55 bonds, 7 residues, 1 model selected
> color sel purple
> show sel
> color byhetero
> select #1 :238,246,255,262,265,296,226
71 atoms, 65 bonds, 9 residues, 1 model selected
> color sel purple
> color byhetero
> select #1/A:226
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
Drag select of 1 atoms
> hide sel atoms
> select clear
> show #2 models
> hbonds #2#!1 reveal true
2575 hydrogen bonds found
> delete /F
> delete :HOH
> select #1 :238,246,255,262,265,296,226
69 atoms, 65 bonds, 1 pseudobond, 7 residues, 2 models selected
> color sel red
> hide #!1 models
> select add #1
2744 atoms, 2800 bonds, 324 pseudobonds, 349 residues, 4 models selected
> select subtract #1
Nothing selected
> show #!1 models
> hide #!1 models
> show #2 cartoons
> color #2/A purple
> select #2 :238,246,255,262,265,296,226
Nothing selected
> select #2 :27,35,44,51,54,85,15
116 atoms, 107 bonds, 1 pseudobond, 13 residues, 2 models selected
> select #2 :27,35,44,51,54,85,15,50
133 atoms, 125 bonds, 2 pseudobonds, 15 residues, 2 models selected
> select #2/A :27,35,44,51,54,85,15,50,55
86 atoms, 83 bonds, 3 pseudobonds, 9 residues, 2 models selected
> select #2/A :35,44,51,54,85,15,50,55
80 atoms, 78 bonds, 3 pseudobonds, 8 residues, 2 models selected
> select #2/A :35,44,51,54,15,50,55
68 atoms, 66 bonds, 3 pseudobonds, 7 residues, 2 models selected
> select #2/A :35,44,51,54,15,50,55,53
76 atoms, 74 bonds, 3 pseudobonds, 8 residues, 2 models selected
> hide sel atoms
> hide #2 atoms
> ~hbonds
> select #2/A :35,44,51,54,15,50,55,53
76 atoms, 74 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #2/B:42
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hbonds sel reveal true
11 hydrogen bonds found
> select #2/A :35,44,51,54,15,50,55,53
76 atoms, 74 bonds, 8 residues, 1 model selected
> hbonds sel reveal true
43 hydrogen bonds found
> select clear
Drag select of 5 residues
> show sel atoms
> hbonds sel reveal true
8 hydrogen bonds found
> ui mousemode right distance
> ui mousemode right select
> select clear
> ui mousemode right distance
> distance #2/A:54@OH #2/B:36@SD
Distance between BFT_Minibinder_3.pdb #2/A TYR 54 OH and /B MET 36 SD: 3.392Å
> hide #!5 models
> hide #5.1 models
> hide #4 models
> ui mousemode right select
Drag select of 1 residues
> hide sel cartoons
> select #2/B:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/B:57@C
1 atom, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select #2/B:57
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> show sel atoms
> select #2/B:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:57
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
Populating font family aliases took 149 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> swapaa interactive sel THR rotLib Dunbrack
BFT_Minibinder_3.pdb #2/B THR 57: phi -136.0, psi none trans
Changed 12 bond radii
> swapaa #!2/B:57 THR criteria 3 rotLib Dunbrack retain false
Using Dunbrack library
BFT_Minibinder_3.pdb #!2/B THR 57: phi -136.0, psi none trans
Applying THR rotamer (chi angles: -173.3) to BFT_Minibinder_3.pdb #!2/B THR 57
> select clear
> ui mousemode right distance
> distance #2/A:35@OD1 #2/B:57@OG1
Distance between BFT_Minibinder_3.pdb #2/A ASN 35 OD1 and /B THR 57 OG1:
3.186Å
> ui mousemode right select
> select #2/B:57
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> ui mousemode right distance
> distance #2/A:44@NZ #2/B:57@OXT
Distance between BFT_Minibinder_3.pdb #2/A LYS 44 NZ and /B THR 57 OXT: 2.213Å
> distance #2/A:44@NZ #2/B:57@OXT
Distance already exists; modify distance properties with 'distance style'
> show sel cartoons
> ui mousemode right select
> select clear
> show #4 models
> select #2/B:39
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:32
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:31
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #2/A:51
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/B:33
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:47
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> hide #4 models
> ui tool show "Side View"
> select #2/B:57
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #2/A:44
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/A:35
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> hide #2 cartoons
> undo
> hide #2 cartoons
> select clear
> ui mousemode right translate
> undo
> select #2/A :35,44,51,54,15,50,55,53
76 atoms, 74 bonds, 8 residues, 1 model selected
> ui mousemode right select
> select #2/B:57@CA
1 atom, 1 residue, 1 model selected
> select #2/B:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:42
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:36
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:25
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> hide #2 cartoons
> select clear
Drag select of 17 atoms, 15 bonds
> select clear
Drag select of 16 atoms, 14 bonds
Drag select of 9 atoms, 8 bonds
Drag select of 4 atoms, 4 bonds
Drag select of 23 atoms, 21 bonds
Drag select of 23 atoms, 22 bonds
> select ~sel
6661 atoms, 6793 bonds, 16 pseudobonds, 849 residues, 8 models selected
> hide sel
Drag select of 8 atoms, 7 bonds
Drag select of 6 atoms, 5 bonds
Drag select of 14 atoms, 12 bonds
> show sel cartoons
> select clear
> select #2/A:35
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/MB03thr_bftasnlys.png width
> 1800 height 1800 supersample 4 transparentBackground true
Drag select of 19 atoms, 2 residues, 16 bonds
> hide sel atoms
> show sel cartoons
> undo
> select clear
> hide #2 cartoons
> select #2/A :35,44,51,54,15,50,55,53
76 atoms, 74 bonds, 8 residues, 1 model selected
> show sel atoms
> show sel cartoons
> Sel #2/B :46,42,36,25
Unknown command: Sel #2/B :46,42,36,25
> ael #2/B :46,42,36,25
Unknown command: ael #2/B :46,42,36,25
> select #2/B :46,42,36,25
36 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select #2/A:51
11 atoms, 11 bonds, 1 residue, 1 model selected
Drag select of 39 atoms, 7 residues, 35 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 10 atoms, 2 residues, 8 bonds
Drag select of 11 atoms, 2 residues, 9 bonds
> hide sel atoms
> hide sel cartoons
> select #2/A:51
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #2/A:50
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> undo
> select #2/A:50
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A :51
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel cartoons
Drag select of 2 residues
> hide sel cartoons
> undo
> select #2/A:51
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 1 atoms, 2 residues, 1 bonds
> hide sel cartoons
> select clear
Drag select of 30 atoms, 1 residues, 31 bonds
> hbonds sel reveal true
14 hydrogen bonds found
> undo
> ~hbonds
> select clear
Drag select of 28 atoms, 1 residues, 30 bonds
Drag select of 29 atoms, 1 residues, 31 bonds
Drag select of 1 atoms, 1 bonds
> select clear
Drag select of 4 atoms, 3 bonds
> hide sel atoms
Drag select of 7 atoms, 6 bonds
Drag select of 8 atoms, 6 bonds
> hide sel atoms
Drag select of 3 atoms, 3 bonds
Drag select of 4 atoms, 3 bonds
> hide sel atoms
> select #2/A:51@CA
1 atom, 1 residue, 1 model selected
> ~hbonds
> ui mousemode right distance
> distance #2/A:51@N #2/B:25@OH
Distance between BFT_Minibinder_3.pdb #2/A PHE 51 N and /B TYR 25 OH: 3.034Å
> distance #2/A:50@N #2/B:25@OH
Distance between BFT_Minibinder_3.pdb #2/A HIS 50 N and /B TYR 25 OH: 4.527Å
> ui mousemode right select
> select clear
Drag select of 14 atoms, 14 bonds
Drag select of 16 atoms, 17 bonds
> show sel cartoons
> select clear
> select #2/A:51
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> ui mousemode right distance
> distance #2/B:25@CD2 #2/A:50@CE1
Distance between BFT_Minibinder_3.pdb #2/B TYR 25 CD2 and /A HIS 50 CE1:
3.616Å
> select ~sel & ##selected
1911 atoms, 1952 bonds, 6 pseudobonds, 243 residues, 2 models selected
> select up
1913 atoms, 1952 bonds, 6 pseudobonds, 244 residues, 2 models selected
> ui mousemode right select
> select clear
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/MB03tyr_bfthis.png width
> 1800 height 1800 supersample 4 transparentBackground true
Drag select of 16 atoms, 2 residues, 16 bonds
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select clear
> select add #2
1922 atoms, 1963 bonds, 6 pseudobonds, 244 residues, 2 models selected
> close #5
> show sel cartoons
> select clear
> select #2/B:57
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A :His
70 atoms, 70 bonds, 7 residues, 1 model selected
> select #1/A @His
Nothing selected
> select #2/A :His
60 atoms, 60 bonds, 6 residues, 1 model selected
> select clear
> select #2/A :35,44,51,54,15,50,55,53
76 atoms, 74 bonds, 8 residues, 1 model selected
> show sel atoms
> select #2/A :35,44,51,54,15,50,55,53
76 atoms, 74 bonds, 8 residues, 1 model selected
> select clear
Drag select of 15 atoms, 29 residues, 13 bonds
> show sel atoms
> select clear
> select #2/A:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:57
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:54
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:15
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:42
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> hide #2 atoms
> hide #2 cartoons
> show #2/A:55,15
> show #2/A:55,15 cartoons
> show #2/B :42
> show #2/B :42 cartoons
> select #2/A:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/minibinder_bftinteractions.cxs
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/MB03asp_bftlysthr.png width
> 1800 height 1800 supersample 4 transparentBackground true
> hide #2 atoms
> show #2 cartoons
> select #2/A :35,44,51,54,15,50,55,53
76 atoms, 74 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> hbonds #2 reveal true
985 hydrogen bonds found
> interfaces #2 & ~solvent
1 buried areas: A B 989
> hide #2 atoms
> hide #2 cartoons
> show #2 cartoons
> ~hbonds
> hbonds #2 reveal true
985 hydrogen bonds found
> select #2/B:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:53@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> ~hbonds
> select add #2
1922 atoms, 1963 bonds, 244 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #2/B:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> select #2/A:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> interfaces #2 & ~solvent
1 buried areas: A B 989
> select add #2
1922 atoms, 1963 bonds, 244 residues, 1 model selected
> show sel cartoons
> hbonds sel reveal true
985 hydrogen bonds found
> ~hbonds
> hide sel atoms
> undo
> show sel cartoons
> hide sel atoms
> show sel atoms
> select add #2
1922 atoms, 1963 bonds, 244 residues, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> select #2/C
1 atom, 1 residue, 1 model selected
> show sel surfaces
> hide sel atoms
> hide sel cartoons
> hide sel atoms
> select #2/C
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of BFT_Minibinder_3.pdb_C SES surface, 25 of 44 triangles
> select #2/C:1@ZN
1 atom, 1 residue, 1 model selected
> hide sel
> hide /C
> select clear
Drag select of BFT_Minibinder_3.pdb_C SES surface, 22 of 44 triangles
> select #2/C:1@ZN
1 atom, 1 residue, 1 model selected
> delete sel
> interfaces #2 & ~solvent
1 buried areas: A B 989
> select interfaces #2
Expected an objects specifier or a keyword
> hide /B cartoons
Drag select of 144 atoms, 141 bonds
Drag select of 146 atoms, 142 bonds
> color sel red
> hide sel atoms
> show sel surfaces
> color sel red
> show #2/A surfaces
> select clear
> undo
> color sel green
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:49
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:49
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select #2/A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:101-102
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:49@O
1 atom, 1 residue, 1 model selected
> select #2/A:66
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:66
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:64@CG
1 atom, 1 residue, 1 model selected
Drag select of BFT_Minibinder_3.pdb_A SES surface, 36340 of 157062 triangles
Drag select of BFT_Minibinder_3.pdb_A SES surface, 16801 of 157062 triangles
> select #2/A:101@CD
1 atom, 1 residue, 1 model selected
> select #2/A:101@O
1 atom, 1 residue, 1 model selected
Drag select of BFT_Minibinder_3.pdb_A SES surface, 35472 of 157062 triangles
> color sel purple
> select #2/A:49
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:49
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:66-67
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/A:66-67
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/A:66
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:66
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> color #1/A :64
> color #1/A :64 purple
> color #2/A :64 purple
> select #2/A:108
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:108
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:144
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:144
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:148-149
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:148-149
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:151-152
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:151-152
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:151
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:151
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:158-159
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #2/A:158-159
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #2/A:158
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:158
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red\
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel red
> select #2/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:172-173
16 atoms, 15 bonds, 2 residues, 1 model selected
> color sel red
> select #2/A:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:59
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:59
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:64-65
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:64-65
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:64-65
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:63-64
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #2/A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:78
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:78
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:105
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:105
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:120
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:120
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:150
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:150
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:157
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:157
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:159
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:159
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:164-165
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:164-165
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:164-165
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel purple
> select #2/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:172-173
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft_interactingresiduees_nonconservedresidues_nomb03.png
> width 1800 height 1638 supersample 4 transparentBackground true
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft_nonconservedresidues.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #!2 surfaces
> undo
> show #!2 surfaces
> hide /B surfaces
> select #2/A:44@CD
1 atom, 1 residue, 1 model selected
> select #2/A:35@CB
1 atom, 1 residue, 1 model selected
> select #2/A:35@ND2
1 atom, 1 residue, 1 model selected
> select #2/A:31@NE2
1 atom, 1 residue, 1 model selected
> select #2/A:27@OG
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> hide #!2 surfaces
> show #!2 cartoons
> select ~sel & ##selected
Nothing selected
> hide /B cartoons
> select #2/A:23-38,43-45,65-78,80-82,99-101,134-142,168-178,182-184
468 atoms, 466 bonds, 62 residues, 1 model selected
> select #2/A:7-15,47-55,89-94,104-106,122-126
263 atoms, 265 bonds, 32 residues, 1 model selected
Drag select of 5 residues
> select #2/A:51
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:51-63
102 atoms, 105 bonds, 13 residues, 1 model selected
> select clear
> select #2/A:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:50
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:50
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:50-61
102 atoms, 106 bonds, 12 residues, 1 model selected
> select #2/A:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:50-56
62 atoms, 64 bonds, 7 residues, 1 model selected
> select #2/A:7-15,47-55,89-94,104-106,122-126
263 atoms, 265 bonds, 32 residues, 1 model selected
> select #2/A:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:50-55
55 atoms, 57 bonds, 6 residues, 1 model selected
> select #2/A:10
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:15
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/A:27
13 atoms, 12 bonds, 2 residues, 2 models selected
> select add #2/A:30
21 atoms, 19 bonds, 3 residues, 2 models selected
> select add #2/A:31
30 atoms, 27 bonds, 4 residues, 2 models selected
> select add #2/A:35
38 atoms, 34 bonds, 5 residues, 2 models selected
> select #2/A:44
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:81
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2/A:85
21 atoms, 20 bonds, 2 residues, 2 models selected
> select clear
> select #2/A:44
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2/A:35
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #2/A:31
26 atoms, 23 bonds, 3 residues, 2 models selected
> select add #2/A:30
34 atoms, 30 bonds, 4 residues, 2 models selected
> select add #2/A:27
40 atoms, 35 bonds, 5 residues, 2 models selected
> select add #2/A:23
47 atoms, 42 bonds, 6 residues, 2 models selected
> select add #2/A:15
58 atoms, 52 bonds, 7 residues, 2 models selected
> select add #2/A:81
67 atoms, 60 bonds, 8 residues, 2 models selected
> select add #2/A:85
79 atoms, 72 bonds, 9 residues, 2 models selected
> select add #2/A:10
91 atoms, 84 bonds, 10 residues, 2 models selected
Drag select of 3 residues
> select add #2/A:52
125 atoms, 90 bonds, 14 residues, 2 models selected
> select add #2/A:51
136 atoms, 101 bonds, 15 residues, 2 models selected
> select add #2/A:50
146 atoms, 111 bonds, 16 residues, 2 models selected
> select ~sel
6537 atoms, 6658 bonds, 7 pseudobonds, 834 residues, 5 models selected
> color sel purple
> select clear
> show /B
> color /B #EAAE11
> hide #!2 atoms
> show #!2 cartoons
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft-mb03_1.png width 1800
> height 1800 supersample 4 transparentBackground true
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft-mb03_2.png width 1800
> height 1800 supersample 4 transparentBackground true
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft-mb03_3.png width 1800
> height 1800 supersample 4 transparentBackground true
> select #2/A:81
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> interfaces #!2 & ~solvent
1 buried areas: A B 989
> hbonds #!2 reveal true
986 hydrogen bonds found
> undo
> select clear
> ~hbonds
> color #!2 byhetero
> color /A purple
> color #!2 byhetero
Drag select of 4 atoms, 4 bonds
> show sel surfaces
> undo
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
Drag select of 3 atoms, 3 bonds
> show sel cartoons
Drag select of 4 atoms, 4 bonds
> show sel cartoons
Drag select of 32 atoms, 1 residues, 29 bonds
> show sel cartoons
Drag select of 11 atoms, 9 bonds
> show sel cartoons
> select clear
Drag select of 5 atoms, 2 residues, 3 bonds
> show sel cartoons
Drag select of 9 atoms, 3 residues, 5 bonds
> select clear
> undo
> show sel atoms
> show #2/B cartoons
> select clear
Drag select of 7 atoms, 14 residues, 4 bonds
> select clear
Drag select of 12 atoms, 15 residues, 9 bonds
> show sel cartoons
> select clear
> ui mousemode right distance
> distance #2/B:56@OD1 #2/A:31@OE1
Distance between BFT_Minibinder_3.pdb #2/B ASN 56 OD1 and /A GLN 31 OE1:
4.367Å
> distance #2/B:56@ND2 #2/A:31@NE2
Distance between BFT_Minibinder_3.pdb #2/B ASN 56 ND2 and /A GLN 31 NE2:
4.112Å
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
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 - 89.3
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: MPHG3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 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: 11 days, 22 hours, 44 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
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
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 8 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 |
This ChimeraX crash is caused by a but in the Qt window toolkit that ChimeraX uses and happens on Mac computers with multiple displays when plugging in or unplugging a display or waking from sleep or moving the ChimeraX window between displays. It may be fixed by the newer Qt version (6.8.2) in the ChimeraX daily build.
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Reported by Pooja Srinivas