![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16593 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-14.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
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{
"uptime" : 1300000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 216947,
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"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
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"captureTime" : "2025-01-09 08:45:46.2255 -0800",
"codeSigningMonitor" : 1,
"incident" : "E1D17739-3EF6-459C-94EF-8876BC49D89A",
"pid" : 14463,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-08 11:25:09.8886 -0800",
"procStartAbsTime" : 32632664405694,
"procExitAbsTime" : 33407890496752,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D95E2E94-1371-53D3-9C64-F4D3AB7107CE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "01DCA152-1CDB-B331-3941-F49EA5A3C7E2",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
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"sleepWakeUUID" : "252247E4-690E-4E22-9BB8-8B4498629F1B",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x0000382f95eba108","rawCodes":[1,61777029865736],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000382f95eba108"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":14463},
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===== Log before crash start =====
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
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/udalwadi/Downloads/cryosparc_P692_J33_008_volume_map.mrc
Opened cryosparc_P692_J33_008_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.929, shown at level 0.00787, step 2, values float32
> open /Users/udalwadi/Documents/GTPgS_C_and_D.cif format mmcif
Summary of feedback from opening /Users/udalwadi/Documents/GTPgS_C_and_D.cif
---
warnings | Unknown polymer entity '1' on line 154
Unknown polymer entity '2' on line 13842
Unknown polymer entity '3' on line 24690
Unknown polymer entity '4' on line 35896
Unknown polymer entity '5' on line 45528
Atom H is not in the residue template for GLY /C:8
Atom H is not in the residue template for GLY /D:8
Atom H is not in the residue template for VAL /E:167
Atom H is not in the residue template for VAL /F:167
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for GTPgS_C_and_D.cif #2
---
Chain | Description
A B | No description available
C D | No description available
E F | No description available
G H | No description available
I J | No description available
> fitmap #2 inMap #1
Fit molecule GTPgS_C_and_D.cif (#2) to map
cryosparc_P692_J33_008_volume_map.mrc (#1) using 58650 atoms
average map value = 0.03411, steps = 128
shifted from previous position = 11.9
rotated from previous position = 0.44 degrees
atoms outside contour = 7499, contour level = 0.0078697
Position of GTPgS_C_and_D.cif (#2) relative to
cryosparc_P692_J33_008_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99999670 -0.00256865 0.00006851 7.38156235
0.00256908 0.99997052 -0.00723633 7.67334227
-0.00004992 0.00723649 0.99997382 5.49356136
Axis 0.94235439 0.00771096 0.33452764
Axis point 0.00000000 -346.08557618 1052.36711008
Rotation angle (degrees) 0.43998297
Shift along axis 8.85296468
> style stick
Changed 58650 atom styles
> show cartoons
> color byhetero
> set bgColor white
> hide H
> volume #1 level 0.01103
> volume #1 step 1
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for GTPgS_C_and_D.cif
---
Chain | Description
2.2/A 2.2/B | No description available
2.2/C 2.2/D | No description available
2.2/E 2.2/F | No description available
2.2/G 2.2/H | No description available
2.2/I 2.2/J | No description available
> clipper associate #1 toModel #2
Opened cryosparc_P692_J33_008_volume_map.mrc as #2.1.1.1, grid size
400,400,400, pixel 0.929, shown at step 1, values float32
> isolde restrain distances #2
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> volume #2.1.1.1 level 0.04643
> select clear
3 models selected
> select clear
> select up
44 atoms, 46 bonds, 1 residue, 1 model selected
> view
> view sel
> select clear
> volume #2.1.1.1 level 0.02404
> select up
44 atoms, 46 bonds, 1 residue, 1 model selected
> isolde add ligand GDP
Fetching CCD GDP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GDP/GDP.cif
Deleted the following atoms from residue GDP C1001: HOA2, HOB3, HOB2
> delete atoms (#!2.2 & sel)
> delete bonds (#!2.2 & sel)
> close #2.2.9
> select /C:1000
44 atoms, 1 residue, 1 model selected
> delete atoms (#!2.2 & sel)
> delete bonds (#!2.2 & sel)
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select /D:1000
44 atoms, 46 bonds, 1 residue, 1 model selected
> delete atoms (#!2.2 & sel)
> delete bonds (#!2.2 & sel)
> isolde restrain distances #2
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde add ligand GDP
Deleted the following atoms from residue GDP C1000: HOB3, HOA2, HOB2
> isolde sim start /C:1000
ISOLDE: started sim
> volume #2.1.1.1 level 0.02607
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view /D:273
> select /C,D:273
44 atoms, 42 bonds, 2 residues, 1 model selected
> swapaa sel ALA
Unknown command: isolde swapaa sel ALA
> swapaa sel ALA
Using Dunbrack library
Swapping /C LYS 273 to ALA
Swapping /D LYS 273 to ALA
> select /D:273
5 atoms, 4 bonds, 1 residue, 1 model selected
> open /Users/udalwadi/Documents/GTPgS_C_and_D.cif format mmcif
Summary of feedback from opening /Users/udalwadi/Documents/GTPgS_C_and_D.cif
---
warnings | Unknown polymer entity '1' on line 154
Unknown polymer entity '2' on line 13842
Unknown polymer entity '3' on line 24690
Unknown polymer entity '4' on line 35896
Unknown polymer entity '5' on line 45528
Atom H is not in the residue template for GLY /C:8
Atom H is not in the residue template for GLY /D:8
Atom H is not in the residue template for VAL /E:167
Atom H is not in the residue template for VAL /F:167
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for GTPgS_C_and_D.cif #1
---
Chain | Description
A B | No description available
C D | No description available
E F | No description available
G H | No description available
I J | No description available
> select add #1
58655 atoms, 59176 bonds, 17 pseudobonds, 3739 residues, 5 models selected
> style sel stick
Changed 58655 atom styles
> show sel cartoons
> color sel byhetero
> hide H
> select #1/D:1000
44 atoms, 46 bonds, 1 residue, 1 model selected
> view sel
> hide #!1 models
> select add #1
58650 atoms, 59172 bonds, 17 pseudobonds, 3738 residues, 3 models selected
> show #!1 models
> hide #!2.2 models
> fitmap #1/D inMap #2.1
Fit molecule GTPgS_C_and_D.cif (#1) to map
cryosparc_P692_J33_008_volume_map.mrc (#2.1.1.1) using 5424 atoms
average map value = 0.02321, steps = 392
shifted from previous position = 2.48
rotated from previous position = 20.3 degrees
atoms outside contour = 5081, contour level = 0.026072
Position of GTPgS_C_and_D.cif (#1) relative to
cryosparc_P692_J33_008_volume_map.mrc (#2.1.1.1) coordinates:
Matrix rotation and translation
0.96243988 0.24566774 -0.11557183 -17.97387705
-0.21396434 0.94837271 0.23411208 10.76947640
0.16711896 -0.20059055 0.96531585 11.89537896
Axis -0.62734635 -0.40796862 -0.66332357
Axis point 29.06364720 80.18159740 0.00000000
Rotation angle (degrees) 20.27103309
Shift along axis -1.00824766
> volume #2.1.1.1 level 0.0375
> volume #2.1.1.1 level 0.04207
> select clear
> fitmap # in #2.1
Missing or invalid "atomsOrMap" argument: invalid objects specifier
> fitmap #1 inMap #2.1
Fit molecule GTPgS_C_and_D.cif (#1) to map
cryosparc_P692_J33_008_volume_map.mrc (#2.1.1.1) using 58650 atoms
average map value = 0.02183, steps = 296
shifted from previous position = 2.22
rotated from previous position = 9.6 degrees
atoms outside contour = 58376, contour level = 0.042074
Position of GTPgS_C_and_D.cif (#1) relative to
cryosparc_P692_J33_008_volume_map.mrc (#2.1.1.1) coordinates:
Matrix rotation and translation
0.97633862 0.10903663 -0.18674557 18.28088875
-0.08144467 0.98539510 0.14954349 -5.73107603
0.20032389 -0.13079565 0.97095975 -8.27040892
Axis -0.54489160 -0.75234194 -0.37023607
Axis point 58.09665008 0.00000000 82.98138415
Rotation angle (degrees) 14.90653645
Shift along axis -2.58737017
> volume #2.1.1.1 level 0.02973
> mmaker #1/D to #2/D
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 GTPgS_C_and_D.cif, chain D (#2.2) with GTPgS_C_and_D.cif, chain D
(#1), sequence alignment score = 1770.2
RMSD between 344 pruned atom pairs is 0.000 angstroms; (across all 344 pairs:
0.000)
> view #1/D:1000
> hide #!1 models
> show #!2.2 models
> volume #2.1.1.1 level 0.02643
> isolde add ligand GDP
Deleted the following atoms from residue GDP D1000: HOB2, HOA2, HOB3
> ui mousemode right "rotate selected models"
> view matrix models
> #2.2,0.96766,0.19582,-0.15905,-2.6444,-0.18983,0.98043,0.0522,29.778,0.16616,-0.020319,0.98589,-24.614
> fitmap #2.2 inMap #2
Fit molecule GTPgS_C_and_D.cif (#2.2) to map
cryosparc_P692_J33_008_volume_map.mrc (#2.1.1.1) using 58608 atoms
average map value = 0.04457, steps = 308
shifted from previous position = 1.62
rotated from previous position = 15 degrees
atoms outside contour = 58010, contour level = 0.026435
Position of GTPgS_C_and_D.cif (#2.2) relative to
cryosparc_P692_J33_008_volume_map.mrc (#2.1.1.1) coordinates:
Matrix rotation and translation
0.99996877 -0.00241708 -0.00752456 1.57585499
0.00216242 0.99943068 -0.03366952 5.82058023
0.00760165 0.03365220 0.99940470 -8.60812469
Axis 0.97353363 -0.21873884 0.06622377
Axis point 0.00000000 258.13393714 166.50096746
Rotation angle (degrees) 1.98145133
Shift along axis -0.30910157
> select clear
> select up
40 atoms, 42 bonds, 1 residue, 1 model selected
> isolde sim start #2.2/D:1000
Sim termination reason: None
ISOLDE: stopped sim
> select ::name="GDP"
80 atoms, 84 bonds, 2 residues, 1 model selected
> view sel
> select clear
> select up
40 atoms, 42 bonds, 1 residue, 1 model selected
> isolde sim start #2.2/D:1000
ISOLDE: started sim
> volume #2.1.1.1 level 0.02026
> show #!1 models
> select add #1
58690 atoms, 59214 bonds, 17 pseudobonds, 3739 residues, 4 models selected
> hide sel cartoons
> hide sel atoms
> select ::name="GDP"
80 atoms, 84 bonds, 2 residues, 1 model selected
> show sel atoms
> select ::name="GSP"
88 atoms, 92 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #2/C:1000
40 atoms, 42 bonds, 1 residue, 1 model selected
> view sel
> isolde sim start #2.2/C:1000
ISOLDE: started sim
> hide #!1 models
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #2
58618 atoms, 59140 bonds, 4 pseudobonds, 3738 residues, 22 models selected
> isolde sim start #2.2/A-J
ISOLDE: started sim
> select clear
> select up
40 atoms, 42 bonds, 1 residue, 1 model selected
> select up
5408 atoms, 5461 bonds, 345 residues, 1 model selected
> select down
40 atoms, 42 bonds, 1 residue, 2 models selected
> view sel
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 45 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> fitmap #2.2 inMap #2.1
Fit molecule GTPgS_C_and_D.cif (#2.2) to map
cryosparc_P692_J33_008_volume_map.mrc (#2.1.1.1) using 58618 atoms
average map value = 0.04467, steps = 220
shifted from previous position = 0.973
rotated from previous position = 2.46 degrees
atoms outside contour = 57947, contour level = 0.020265
Position of GTPgS_C_and_D.cif (#2.2) relative to
cryosparc_P692_J33_008_volume_map.mrc (#2.1.1.1) coordinates:
Matrix rotation and translation
0.99989450 -0.00964658 0.01085929 -0.36435762
0.00959934 0.99994427 0.00439428 -2.32137595
-0.01090108 -0.00428958 0.99993138 2.68689623
Axis -0.28640286 0.71768016 0.63475081
Axis point 237.90145715 0.00000000 32.06969077
Rotation angle (degrees) 0.86864957
Shift along axis 0.14385716
> select clear
> view #2.2/D:1000
> show #!1 models
> hide #!1 models
> select #2.2
58618 atoms, 59140 bonds, 4 pseudobonds, 3738 residues, 15 models selected
> isolde sim start #2.2/A-J
ISOLDE: started sim
> show #!1 models
> view #2.2/C:1000
> select clear
> hide #!1 models
> view /B:188
> view /A:188
> view /C:188
> volume #2.1.1.1 level 0.02617
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 13 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select /C
10832 atoms, 10938 bonds, 13 pseudobonds, 690 residues, 3 models selected
> isolde sim start #2.2/C #1/C
ISOLDE: started sim
> select up
117268 atoms, 118312 bonds, 7476 residues, 3 models selected
> select up
117268 atoms, 118312 bonds, 7476 residues, 4 models selected
> select clear
> view /C:188
> view /C:1000
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> mmaker #1/D to #2/C
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 GTPgS_C_and_D.cif, chain C (#2.2) with GTPgS_C_and_D.cif, chain D
(#1), sequence alignment score = 1754
RMSD between 344 pruned atom pairs is 0.301 angstroms; (across all 344 pairs:
0.301)
> show #!1 models
> volume #2.1.1.1 level 0.02238
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /C
10832 atoms, 10938 bonds, 13 pseudobonds, 690 residues, 3 models selected
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> select clear
> show #!1 models
> hide #!1 models
> view /C:273
> show #!1 models
> hide #!2.2 models
> select add #1
58650 atoms, 59172 bonds, 17 pseudobonds, 3738 residues, 3 models selected
> show sel cartoons
> show sel atoms
> show #!2.2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2.2 models
> hide #!1 models
> show #!2.2 models
> show #!1 models
> select subtract #1
Nothing selected
> hide #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 7 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select /D
10832 atoms, 10938 bonds, 690 residues, 2 models selected
> isolde sim start #2.2/D #1/D
ISOLDE: started sim
> select clear
> view /D:1000
> view #2/D:1000
> select /D
10832 atoms, 10938 bonds, 690 residues, 2 models selected
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #2.1.1.1 level 0.02655
> volume #2.1.1.1 level 0.02322
> view /D:111-114
> view #2/D:111-114
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #2/A
6844 atoms, 6917 bonds, 1 pseudobond, 438 residues, 2 models selected
> isolde sim start #2.2/A
ISOLDE: started sim
> view sel
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #2/B
6844 atoms, 6917 bonds, 1 pseudobond, 438 residues, 2 models selected
> isolde sim start #2.2/B
ISOLDE: started sim
> view sel
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #2/E
5603 atoms, 5652 bonds, 359 residues, 1 model selected
> view sel
> isolde sim start #2.2/E
ISOLDE: started sim
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #2/F
5603 atoms, 5652 bonds, 359 residues, 1 model selected
> view sel
> isolde sim start #2.2/F
ISOLDE: started sim
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #2/G
4816 atoms, 4852 bonds, 306 residues, 1 model selected
> view sel
> isolde sim start #2.2/G
ISOLDE: started sim
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> select clear
> view #2G:77-87
Expected an objects specifier or a view name or a keyword
> view #2/G:77-87
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #2/H
4816 atoms, 4852 bonds, 306 residues, 1 model selected
> view sel
> isolde sim start #2.2/H
ISOLDE: started sim
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 4 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #2/C:1000
> view #2/C:273
> show #!1 models
> hide #!1 models
> select #2/H
4816 atoms, 4852 bonds, 306 residues, 1 model selected
> view sel
> select #2/I
6638 atoms, 6688 bonds, 1 pseudobond, 421 residues, 2 models selected
> view sel
> isolde sim start #2.2/I
ISOLDE: started sim
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #2/J
6638 atoms, 6688 bonds, 1 pseudobond, 421 residues, 2 models selected
> view sel
> isolde sim start #2.2/J
ISOLDE: started sim
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /Users/udalwadi/Documents/241212_J33-eIF2B_bK273A_GDP.cif relModel
> #2.1.1.1.1
Not saving entity_poly_seq for non-authoritative sequences
No model chosen to save relative to
> save /Users/udalwadi/Documents/241212_J33-eIF2B_bK273A_GDP.cif models #2
> relModel #2.1.1.1.1
Not saving entity_poly_seq for non-authoritative sequences
> select #2/H
4816 atoms, 4852 bonds, 306 residues, 1 model selected
> view sel
> isolde restrain distances sel
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde sim start #2.2/H
ISOLDE: started sim
> select up
58618 atoms, 59140 bonds, 3738 residues, 2 models selected
> select #2/H:72-82
187 atoms, 188 bonds, 11 residues, 1 model selected
> view sel
> select up
299 atoms, 300 bonds, 20 residues, 2 models selected
> select clear
> select #2/H:72-82
187 atoms, 188 bonds, 11 residues, 1 model selected
> view sel
> select clear
> close #2.2.1
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /Users/udalwadi/Documents/241212_J33-eIF2B_bK273A_GDP.cif models #2
> relModel #2.1.1.1.1
Not saving entity_poly_seq for non-authoritative sequences
> isolde restrain distances #2
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select #2.2
58618 atoms, 59140 bonds, 4 pseudobonds, 3738 residues, 15 models selected
> isolde sim start #2.2/A-J
ISOLDE: started sim
> select clear
> select #2/D
5408 atoms, 5461 bonds, 345 residues, 1 model selected
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 12 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #2/D
5408 atoms, 5461 bonds, 345 residues, 1 model selected
> isolde sim start #2.2/D
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #2/D,F,H
15827 atoms, 15965 bonds, 1010 residues, 1 model selected
> isolde sim start #2.2/D,F,H
ISOLDE: started sim
> volume #2.1.1.1 level 0.02153
> isolde release distances #2.2&sel groupName "Reference Distance Restraints"
> select clear
> close #2.2.1
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 11 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /Users/udalwadi/Documents/241212_J33-eIF2B_bK273A_GDP.cif models #2
> relModel #2.1.1.1.1
Not saving entity_poly_seq for non-authoritative sequences
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
still retrieving bundle list from toolshed
> isolde shorthand
Error running startup command 'isolde shorthand': Unknown command: isolde
shorthand
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGR3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 84 days, 17 hours, 56 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
HP Z27k G3:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
HP Z27k G3:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 10 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 , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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