![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17405 closed defect (can't reproduce)
Crash during auto-completion
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1.1-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.
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{
"uptime" : 2400000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 117663,
"osVersion" : {
"train" : "macOS 14.1.1",
"build" : "23B81",
"releaseType" : "User"
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"captureTime" : "2025-04-16 18:18:56.7418 -0400",
"codeSigningMonitor" : 1,
"incident" : "6049CD79-973F-4A9F-AE78-6F8C4C402639",
"pid" : 2457,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-16 18:05:30.9481 -0400",
"procStartAbsTime" : 59708674221139,
"procExitAbsTime" : 59728013027520,
"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":"F5319B2A-99FE-5DFC-A089-2820E639FE6C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "216F332D-5F24-FDDF-13EF-8C5782DCD983",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"ARAA1MADX9aQBYCSARAA1MADX9awBYCSARAA1MADX9bQBYCSARAA1A==","atPC":"wANf1vAFgJIBEADUwANf1hAGgJIBEADUwANf1jAGgJIBEADUwANf1g=="},
"sip" : "enabled",
"sroute_id" : 12,
"exception" : {"port":0,"signal":"SIGKILL","guardId":0,"codes":"0x0000000000000000, 0x0000000000000000","violations":["INVALID_OPTIONS"],"message":" INVALID_OPTIONS on mach port 0 (guarded with 0x0000000000000000)","subtype":"GUARD_TYPE_MACH_PORT","type":"EXC_GUARD","rawCodes":[0,0]},
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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/shoichitachiyama/Downloads/cryosparc_P3_J166_002_volume_map_sharp.mrc
Opened cryosparc_P3_J166_002_volume_map_sharp.mrc as #1, grid size
448,448,448, pixel 1.14, shown at level 0.0887, step 2, values float32
> volume #1 level 0.05387
> volume #1 step 1
> volume #1 level 0.01639
> close #1
> open
> /Users/shoichitachiyama/Downloads/cryosparc_P3_J158_class_01_00042_volume_sharp.mrc
Opened cryosparc_P3_J158_class_01_00042_volume_sharp.mrc as #1, grid size
120,120,120, pixel 4.27, shown at level 0.636, step 1, values float32
> volume #1 level 0.03766
> volume #1 level 0.1706
> open /Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-
> documents/P_aeruginosa_T4pili/Segmentation_02232025/T4pili_model.pdb
Summary of feedback from opening
/Users/shoichitachiyama/Library/CloudStorage/OneDrive-
YaleUniversity/Jun_Lab_documents/Project-
documents/P_aeruginosa_T4pili/Segmentation_02232025/T4pili_model.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 7 GLY A 93 1 87
Start residue of secondary structure not found: HELIX 2 2 ARG A 95 ARG A 107 1
13
Start residue of secondary structure not found: HELIX 3 3 ASN A 134 ASP A 145
1 12
Start residue of secondary structure not found: HELIX 4 4 GLU A 183 GLN A 194
1 12
Start residue of secondary structure not found: HELIX 6 6 LEU B 3 SER B 9 1 7
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 LEU B 100 GLN B 102
1 3
Start residue of secondary structure not found: HELIX 15 15 ASP B 106 GLU B
108 1 3
Start residue of secondary structure not found: HELIX 16 16 VAL B 109 GLY B
122 1 14
Start residue of secondary structure not found: HELIX 17 17 TYR B 154 GLY B
163 1 10
Start residue of secondary structure not found: HELIX 18 18 VAL B 164 SER B
166 1 3
Start residue of secondary structure not found: HELIX 19 19 ASP B 202 LYS B
206 1 5
Start residue of secondary structure not found: HELIX 20 20 ARG C 2 GLY C 17 1
16
16 messages similar to the above omitted
End residue of secondary structure not found: SHEET 13 13 1 LYS C 139 SER C
144 0
Start residue of secondary structure not found: SHEET 14 14 1 LYS C 147 PRO C
155 0
Start residue of secondary structure not found: SHEET 15 15 1 TRP C 161 THR C
169 0
Start residue of secondary structure not found: HELIX 1 1 LEU A 7 GLY A 93 1
87
Start residue of secondary structure not found: HELIX 2 2 ARG A 95 ARG A 107 1
13
Start residue of secondary structure not found: HELIX 3 3 ASN A 134 ASP A 145
1 12
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 LEU B 100 GLN B 102
1 3
Start residue of secondary structure not found: HELIX 15 15 ASP B 106 GLU B
108 1 3
Start residue of secondary structure not found: HELIX 16 16 VAL B 109 GLY B
122 1 14
Start residue of secondary structure not found: HELIX 17 17 TYR B 154 GLY B
163 1 10
Start residue of secondary structure not found: HELIX 18 18 VAL B 164 SER B
166 1 3
Start residue of secondary structure not found: HELIX 19 19 ASP B 202 LYS B
206 1 5
Start residue of secondary structure not found: HELIX 20 20 ARG C 2 GLY C 17 1
16
16 messages similar to the above omitted
End residue of secondary structure not found: SHEET 13 13 1 LYS C 139 SER C
144 0
Start residue of secondary structure not found: SHEET 14 14 1 LYS C 147 PRO C
155 0
Start residue of secondary structure not found: SHEET 15 15 1 TRP C 161 THR C
169 0
Start residue of secondary structure not found: HELIX 1 1 LEU A 7 GLY A 93 1
87
Start residue of secondary structure not found: HELIX 2 2 ARG A 95 ARG A 107 1
13
Start residue of secondary structure not found: HELIX 3 3 ASN A 134 ASP A 145
1 12
75 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 LEU A 7 GLY A 93 1 87
Start residue of secondary structure not found: HELIX 2 2 ARG A 95 ARG A 107 1
13
Start residue of secondary structure not found: HELIX 3 3 ASN A 134 ASP A 145
1 12
Start residue of secondary structure not found: HELIX 4 4 GLU A 183 GLN A 194
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY A 195 LYS A 197
1 3
Start residue of secondary structure not found: HELIX 6 6 LEU B 3 SER B 9 1 7
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 LEU B 100 GLN B 102
1 3
End residue of secondary structure not found: HELIX 15 15 ASP B 106 GLU B 108
1 3
Start residue of secondary structure not found: HELIX 16 16 VAL B 109 GLY B
122 1 14
Start residue of secondary structure not found: HELIX 17 17 TYR B 154 GLY B
163 1 10
Start residue of secondary structure not found: HELIX 18 18 VAL B 164 SER B
166 1 3
Start residue of secondary structure not found: HELIX 19 19 ASP B 202 LYS B
206 1 5
Start residue of secondary structure not found: HELIX 20 20 ARG C 2 GLY C 17 1
16
8 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 GLU B 126 LEU B 132
0
End residue of secondary structure not found: SHEET 6 6 1 TYR B 141 GLY B 152
0
Start residue of secondary structure not found: SHEET 7 7 1 VAL B 171 LEU B
173 0
Start residue of secondary structure not found: SHEET 8 8 1 PHE B 176 PRO B
180 0
End residue of secondary structure not found: SHEET 9 9 1 LEU B 189 TYR B 200
0
Start residue of secondary structure not found: SHEET 10 10 1 GLU C 103 ASN C
110 0
Start residue of secondary structure not found: SHEET 11 11 1 GLY C 113 GLY C
120 0
Start residue of secondary structure not found: SHEET 12 12 1 GLY C 123 ARG C
128 0
Start residue of secondary structure not found: SHEET 13 13 1 LYS C 139 SER C
144 0
Start residue of secondary structure not found: SHEET 14 14 1 LYS C 147 PRO C
155 0
1 messages similar to the above omitted
Chain information for T4pili_model.pdb
---
Chain | Description
2.1/A 2.2/A 2.1/B 2.2/B 2.1/C 2.2/C 2.1/D 2.2/D 2.1/E 2.2/E 2.1/F 2.2/F 2.1/G 2.2/G | No description available
2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A | No description available
2.12/A 2.12/B 2.12/C | No description available
2.3/B 2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B | No description available
2.3/C 2.4/C 2.5/C 2.6/C 2.7/C 2.8/C 2.9/C | No description available
2.10/a 2.11/a 2.10/b 2.11/b 2.10/c 2.11/c 2.10/d 2.11/d 2.10/e 2.11/e 2.10/f 2.11/f 2.10/g 2.11/g 2.10/h 2.11/h 2.10/i 2.11/i 2.10/j 2.11/j 2.10/k 2.11/k 2.10/l 2.11/l 2.10/m 2.11/m 2.10/n 2.11/n 2.10/o 2.11/o 2.10/p 2.11/p | No description available
> select add #2
183828 atoms, 186039 bonds, 19747 residues, 13 models selected
> hide sel atoms
> show sel cartoons
> select subtract #2.1
145727 atoms, 147378 bonds, 14749 residues, 12 models selected
> select add #2.1
183828 atoms, 186039 bonds, 19747 residues, 13 models selected
> select subtract #2.12
175221 atoms, 177297 bonds, 18625 residues, 12 models selected
> select subtract #2.11
141493 atoms, 143329 bonds, 16337 residues, 11 models selected
> select add #2.11
175221 atoms, 177297 bonds, 18625 residues, 12 models selected
> select subtract #2.3
170712 atoms, 172720 bonds, 18046 residues, 11 models selected
> select add #2.3
175221 atoms, 177297 bonds, 18625 residues, 12 models selected
> hide #2.12 models
> hide #!1 models
> show #2.12 models
> hide #2.12 models
> save /Users/shoichitachiyama/Desktop/Pa-T4pili-model.pdb selectedOnly true
> open /Users/shoichitachiyama/Desktop/Pa-T4pili-model.pdb
Summary of feedback from opening /Users/shoichitachiyama/Desktop/Pa-T4pili-
model.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 195 LYS A 197 1 3
Start residue of secondary structure not found: HELIX 1 1 GLY A 195 LYS A 197
1 3
Chain information for Pa-T4pili-model.pdb
---
Chain | Description
3.1/A 3.2/A 3.1/B 3.2/B 3.1/C 3.2/C 3.1/D 3.2/D 3.1/E 3.2/E 3.1/F 3.2/F 3.1/G 3.2/G | No description available
3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A | No description available
3.3/B 3.4/B 3.5/B 3.6/B 3.7/B 3.8/B 3.9/B | No description available
3.3/C 3.4/C 3.5/C 3.6/C 3.7/C 3.8/C 3.9/C | No description available
3.10/a 3.11/a 3.10/b 3.11/b 3.10/c 3.11/c 3.10/d 3.11/d 3.10/e 3.11/e 3.10/f 3.11/f 3.10/g 3.11/g 3.10/h 3.11/h 3.10/i 3.11/i 3.10/j 3.11/j 3.10/k 3.11/k 3.10/l 3.11/l 3.10/m 3.11/m 3.10/n 3.11/n 3.10/o 3.11/o 3.10/p 3.11/p | No description available
> hide #!2 models
> select add #2
183828 atoms, 186039 bonds, 19747 residues, 13 models selected
> show #!1 models
> select subtract #2
Nothing selected
> select add #3
175221 atoms, 177297 bonds, 18625 residues, 12 models selected
> hide sel atoms
> show sel cartoons
> color #1 #b2b2b2a6 models
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-8.6797,0,1,0,-112.87,0,0,1,-67.443
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.80602,-0.46568,0.36534,117.91,-0.47941,-0.87564,-0.058462,822.16,0.34713,-0.12802,-0.92904,530.59
> view matrix models
> #3,0.61774,0.78632,0.0099479,-164.52,0.78562,-0.61653,-0.051811,237.86,-0.034607,0.039821,-0.99861,639.33
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.61774,0.78632,0.0099479,-285.79,0.78562,-0.61653,-0.051811,223.13,-0.034607,0.039821,-0.99861,590.1
> view matrix models
> #3,0.61774,0.78632,0.0099479,-294.96,0.78562,-0.61653,-0.051811,210.01,-0.034607,0.039821,-0.99861,588.15
> volume #1 level 0.1844
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.11 models
> show #3.11 models
> combine #3
Remapping chain ID 'A' in Pa-T4pili-model.pdb #3.2 to 'H'
Remapping chain ID 'B' in Pa-T4pili-model.pdb #3.2 to 'I'
Remapping chain ID 'C' in Pa-T4pili-model.pdb #3.2 to 'J'
Remapping chain ID 'D' in Pa-T4pili-model.pdb #3.2 to 'K'
Remapping chain ID 'E' in Pa-T4pili-model.pdb #3.2 to 'L'
Remapping chain ID 'F' in Pa-T4pili-model.pdb #3.2 to 'M'
Remapping chain ID 'G' in Pa-T4pili-model.pdb #3.2 to 'N'
Remapping chain ID 'A' in Pa-T4pili-model.pdb #3.3 to 'O'
Remapping chain ID 'B' in Pa-T4pili-model.pdb #3.3 to 'P'
Remapping chain ID 'C' in Pa-T4pili-model.pdb #3.3 to 'Q'
Remapping chain ID 'A' in Pa-T4pili-model.pdb #3.4 to 'R'
Remapping chain ID 'B' in Pa-T4pili-model.pdb #3.4 to 'S'
Remapping chain ID 'C' in Pa-T4pili-model.pdb #3.4 to 'T'
Remapping chain ID 'A' in Pa-T4pili-model.pdb #3.5 to 'U'
Remapping chain ID 'B' in Pa-T4pili-model.pdb #3.5 to 'V'
Remapping chain ID 'C' in Pa-T4pili-model.pdb #3.5 to 'W'
Remapping chain ID 'A' in Pa-T4pili-model.pdb #3.6 to 'X'
Remapping chain ID 'B' in Pa-T4pili-model.pdb #3.6 to 'Y'
Remapping chain ID 'C' in Pa-T4pili-model.pdb #3.6 to 'Z'
Remapping chain ID 'A' in Pa-T4pili-model.pdb #3.7 to 'a'
Remapping chain ID 'B' in Pa-T4pili-model.pdb #3.7 to 'b'
Remapping chain ID 'C' in Pa-T4pili-model.pdb #3.7 to 'c'
Remapping chain ID 'A' in Pa-T4pili-model.pdb #3.8 to 'd'
Remapping chain ID 'B' in Pa-T4pili-model.pdb #3.8 to 'e'
Remapping chain ID 'C' in Pa-T4pili-model.pdb #3.8 to 'f'
Remapping chain ID 'A' in Pa-T4pili-model.pdb #3.9 to 'g'
Remapping chain ID 'B' in Pa-T4pili-model.pdb #3.9 to 'h'
Remapping chain ID 'C' in Pa-T4pili-model.pdb #3.9 to 'i'
Remapping chain ID 'a' in Pa-T4pili-model.pdb #3.10 to 'q'
Remapping chain ID 'b' in Pa-T4pili-model.pdb #3.10 to 'r'
Remapping chain ID 'c' in Pa-T4pili-model.pdb #3.10 to 's'
Remapping chain ID 'd' in Pa-T4pili-model.pdb #3.10 to 't'
Remapping chain ID 'e' in Pa-T4pili-model.pdb #3.10 to 'u'
Remapping chain ID 'f' in Pa-T4pili-model.pdb #3.10 to 'v'
Remapping chain ID 'g' in Pa-T4pili-model.pdb #3.10 to 'w'
Remapping chain ID 'h' in Pa-T4pili-model.pdb #3.10 to 'x'
Remapping chain ID 'i' in Pa-T4pili-model.pdb #3.10 to 'y'
Remapping chain ID 'a' in Pa-T4pili-model.pdb #3.11 to 'z'
Remapping chain ID 'b' in Pa-T4pili-model.pdb #3.11 to '1'
Remapping chain ID 'c' in Pa-T4pili-model.pdb #3.11 to '2'
Remapping chain ID 'd' in Pa-T4pili-model.pdb #3.11 to '3'
Remapping chain ID 'e' in Pa-T4pili-model.pdb #3.11 to '4'
Remapping chain ID 'f' in Pa-T4pili-model.pdb #3.11 to '5'
Remapping chain ID 'g' in Pa-T4pili-model.pdb #3.11 to '6'
Remapping chain ID 'h' in Pa-T4pili-model.pdb #3.11 to '7'
Remapping chain ID 'i' in Pa-T4pili-model.pdb #3.11 to '8'
Remapping chain ID 'j' in Pa-T4pili-model.pdb #3.11 to '9'
Remapping chain ID 'k' in Pa-T4pili-model.pdb #3.11 to '0'
Remapping chain ID 'l' in Pa-T4pili-model.pdb #3.11 to 'AA'
Remapping chain ID 'm' in Pa-T4pili-model.pdb #3.11 to 'AB'
Remapping chain ID 'n' in Pa-T4pili-model.pdb #3.11 to 'AC'
Remapping chain ID 'o' in Pa-T4pili-model.pdb #3.11 to 'AD'
Remapping chain ID 'p' in Pa-T4pili-model.pdb #3.11 to 'AE'
> hide #!3 models
> select subtract #3
Nothing selected
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #4 inMap #1
Fit molecule combination (#4) to map
cryosparc_P3_J158_class_01_00042_volume_sharp.mrc (#1) using 175221 atoms
average map value = 0.2697, steps = 120
shifted from previous position = 20.7
rotated from previous position = 12 degrees
atoms outside contour = 73778, contour level = 0.1844
Position of combination (#4) relative to
cryosparc_P3_J158_class_01_00042_volume_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.73355816 0.67109284 -0.10736301 -261.72186139
0.66348419 -0.74136835 -0.10080521 314.05592716
-0.14724520 0.00271282 -0.98909630 633.55497280
Axis 0.93095433 0.35866689 -0.06842582
Axis point 0.00000000 198.15625441 312.78612779
Rotation angle (degrees) 176.81283703
Shift along axis -174.36115980
> fitmap #4 inMap #1
Fit molecule combination (#4) to map
cryosparc_P3_J158_class_01_00042_volume_sharp.mrc (#1) using 175221 atoms
average map value = 0.2697, steps = 180
shifted from previous position = 0.222
rotated from previous position = 0.0887 degrees
atoms outside contour = 73685, contour level = 0.1844
Position of combination (#4) relative to
cryosparc_P3_J158_class_01_00042_volume_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.73384698 0.67097242 -0.10613493 -262.12590349
0.66349883 -0.74147664 -0.09990839 313.83876983
-0.14573235 0.00289706 -0.98931981 633.09076365
Axis 0.93103272 0.35860441 -0.06768277
Axis point 0.00000000 198.18300818 312.60142421
Rotation angle (degrees) 176.83506567
Shift along axis -174.35316467
> view orient
> turn x 90
> select add #4
175221 atoms, 177297 bonds, 18625 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.74491,0.66715,-0.0042783,-303.6,0.6635,-0.74148,-0.099908,313.84,-0.069826,0.071584,-0.99499,579.03
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.74491,0.66715,-0.0042783,-292.51,0.6635,-0.74148,-0.099908,313.84,-0.069826,0.071584,-0.99499,579.27
> view orient
> ui tool show "Side View"
> surface dust #1 size 42.7
> color #1 #808080a6 models
> color #1 #808080c6 models
> color #1 #808080c8 models
> color #1 #808080c7 models
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.77772,0.62855,-0.0093577,-288.16,0.62473,-0.77447,-0.099561,341.6,-0.069826,0.071584,-0.99499,579.27
> view matrix models
> #4,0.77554,0.63007,-0.039397,-276.5,0.62994,-0.77645,-0.017108,309.04,-0.041369,-0.01155,-0.99908,602.35
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.77554,0.63007,-0.039397,-276.03,0.62994,-0.77645,-0.017108,314.72,-0.041369,-0.01155,-0.99908,602.35
> select clear
> view orient
> turn x 90
> select add #4
175221 atoms, 177297 bonds, 18625 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.7766,0.62999,0.0033099,-292.63,0.62994,-0.77645,-0.017108,314.72,-0.0082078,0.015371,-0.99985,579.29
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.7766,0.62999,0.0033099,-288.84,0.62994,-0.77645,-0.017108,314.72,-0.0082078,0.015371,-0.99985,578.97
> turn y 10
> view matrix models
> #4,0.7766,0.62999,0.0033099,-287.51,0.62994,-0.77645,-0.017108,318.37,-0.0082078,0.015371,-0.99985,579.67
> turn y 10
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.77658,0.63002,-0.00012918,-286.21,0.63001,-0.77655,-0.0076591,314.8,-0.0049257,0.0058665,-0.99997,582.17
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.77658,0.63002,-0.00012918,-286.61,0.63001,-0.77655,-0.0076591,315.91,-0.0049257,0.0058665,-0.99997,581.77
> split #4
Split combination (#4) into 67 models
Chain information for combination 0 #4.1
---
Chain | Description
0 | No description available
Chain information for combination 1 #4.2
---
Chain | Description
1 | No description available
Chain information for combination 2 #4.3
---
Chain | Description
2 | No description available
Chain information for combination 3 #4.4
---
Chain | Description
3 | No description available
Chain information for combination 4 #4.5
---
Chain | Description
4 | No description available
Chain information for combination 5 #4.6
---
Chain | Description
5 | No description available
Chain information for combination 6 #4.7
---
Chain | Description
6 | No description available
Chain information for combination 7 #4.8
---
Chain | Description
7 | No description available
Chain information for combination 8 #4.9
---
Chain | Description
8 | No description available
Chain information for combination 9 #4.10
---
Chain | Description
9 | No description available
Chain information for combination A #4.11
---
Chain | Description
A | No description available
Chain information for combination AA #4.12
---
Chain | Description
AA | No description available
Chain information for combination AB #4.13
---
Chain | Description
AB | No description available
Chain information for combination AC #4.14
---
Chain | Description
AC | No description available
Chain information for combination AD #4.15
---
Chain | Description
AD | No description available
Chain information for combination AE #4.16
---
Chain | Description
AE | No description available
Chain information for combination B #4.17
---
Chain | Description
B | No description available
Chain information for combination C #4.18
---
Chain | Description
C | No description available
Chain information for combination D #4.19
---
Chain | Description
D | No description available
Chain information for combination E #4.20
---
Chain | Description
E | No description available
Chain information for combination F #4.21
---
Chain | Description
F | No description available
Chain information for combination G #4.22
---
Chain | Description
G | No description available
Chain information for combination H #4.23
---
Chain | Description
H | No description available
Chain information for combination I #4.24
---
Chain | Description
I | No description available
Chain information for combination J #4.25
---
Chain | Description
J | No description available
Chain information for combination K #4.26
---
Chain | Description
K | No description available
Chain information for combination L #4.27
---
Chain | Description
L | No description available
Chain information for combination M #4.28
---
Chain | Description
M | No description available
Chain information for combination N #4.29
---
Chain | Description
N | No description available
Chain information for combination O #4.30
---
Chain | Description
O | No description available
Chain information for combination P #4.31
---
Chain | Description
P | No description available
Chain information for combination Q #4.32
---
Chain | Description
Q | No description available
Chain information for combination R #4.33
---
Chain | Description
R | No description available
Chain information for combination S #4.34
---
Chain | Description
S | No description available
Chain information for combination T #4.35
---
Chain | Description
T | No description available
Chain information for combination U #4.36
---
Chain | Description
U | No description available
Chain information for combination V #4.37
---
Chain | Description
V | No description available
Chain information for combination W #4.38
---
Chain | Description
W | No description available
Chain information for combination X #4.39
---
Chain | Description
X | No description available
Chain information for combination Y #4.40
---
Chain | Description
Y | No description available
Chain information for combination Z #4.41
---
Chain | Description
Z | No description available
Chain information for combination a #4.42
---
Chain | Description
a | No description available
Chain information for combination b #4.43
---
Chain | Description
b | No description available
Chain information for combination c #4.44
---
Chain | Description
c | No description available
Chain information for combination d #4.45
---
Chain | Description
d | No description available
Chain information for combination e #4.46
---
Chain | Description
e | No description available
Chain information for combination f #4.47
---
Chain | Description
f | No description available
Chain information for combination g #4.48
---
Chain | Description
g | No description available
Chain information for combination h #4.49
---
Chain | Description
h | No description available
Chain information for combination i #4.50
---
Chain | Description
i | No description available
Chain information for combination j #4.51
---
Chain | Description
j | No description available
Chain information for combination k #4.52
---
Chain | Description
k | No description available
Chain information for combination l #4.53
---
Chain | Description
l | No description available
Chain information for combination m #4.54
---
Chain | Description
m | No description available
Chain information for combination n #4.55
---
Chain | Description
n | No description available
Chain information for combination o #4.56
---
Chain | Description
o | No description available
Chain information for combination p #4.57
---
Chain | Description
p | No description available
Chain information for combination q #4.58
---
Chain | Description
q | No description available
Chain information for combination r #4.59
---
Chain | Description
r | No description available
Chain information for combination s #4.60
---
Chain | Description
s | No description available
Chain information for combination t #4.61
---
Chain | Description
t | No description available
Chain information for combination u #4.62
---
Chain | Description
u | No description available
Chain information for combination v #4.63
---
Chain | Description
v | No description available
Chain information for combination w #4.64
---
Chain | Description
w | No description available
Chain information for combination x #4.65
---
Chain | Description
x | No description available
Chain information for combination y #4.66
---
Chain | Description
y | No description available
Chain information for combination z #4.67
---
Chain | Description
z | No description available
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #4.2 models
> hide #4.3 models
> show #4.3 models
> hide #!1 models
> show #4.2 models
> show #4.1 models
> hide #4.11 models
> show #4.11 models
> hide #4.2 models
> show #4.2 models
> hide #4.1 models
> hide #4.67 models
> show #4.67 models
> hide #4.66 models
> show #4.66 models
> hide #4.57 models
> show #4.57 models
Drag select of 623 residues
> hide #4.10 models
> hide #4.12 models
> hide #4.13 models
> hide #4.14 models
> hide #4.15 models
> hide #4.16 models
> select clear
> select add #4.2
2108 atoms, 2123 bonds, 143 residues, 1 model selected
> select add #4.3
4216 atoms, 4246 bonds, 286 residues, 2 models selected
> select add #4.4
6324 atoms, 6369 bonds, 429 residues, 3 models selected
> select add #4.5
8432 atoms, 8492 bonds, 572 residues, 4 models selected
> select add #4.6
10540 atoms, 10615 bonds, 715 residues, 5 models selected
> select add #4.7
12648 atoms, 12738 bonds, 858 residues, 6 models selected
> select add #4.8
14756 atoms, 14861 bonds, 1001 residues, 7 models selected
> select add #4.9
16864 atoms, 16984 bonds, 1144 residues, 8 models selected
> select add #4.11
22307 atoms, 22507 bonds, 1858 residues, 9 models selected
> select add #4.17
27750 atoms, 28030 bonds, 2572 residues, 10 models selected
> select add #4.18
33193 atoms, 33553 bonds, 3286 residues, 11 models selected
> select add #4.19
38636 atoms, 39076 bonds, 4000 residues, 12 models selected
> select add #4.20
44079 atoms, 44599 bonds, 4714 residues, 13 models selected
> select add #4.21
49522 atoms, 50122 bonds, 5428 residues, 14 models selected
> select add #4.22
54965 atoms, 55645 bonds, 6142 residues, 15 models selected
> select add #4.23
60408 atoms, 61168 bonds, 6856 residues, 16 models selected
> select add #4.25
65851 atoms, 66691 bonds, 7570 residues, 17 models selected
> select add #4.24
71294 atoms, 72214 bonds, 8284 residues, 18 models selected
> select add #4.27
76737 atoms, 77737 bonds, 8998 residues, 19 models selected
> select add #4.26
82180 atoms, 83260 bonds, 9712 residues, 20 models selected
> select add #4.29
87623 atoms, 88783 bonds, 10426 residues, 21 models selected
> select add #4.28
93066 atoms, 94306 bonds, 11140 residues, 22 models selected
> select add #4.30
94628 atoms, 95886 bonds, 11338 residues, 23 models selected
> select add #4.31
96233 atoms, 97517 bonds, 11545 residues, 24 models selected
> select add #4.32
97575 atoms, 98883 bonds, 11719 residues, 25 models selected
> select add #4.33
99137 atoms, 100463 bonds, 11917 residues, 26 models selected
> select add #4.34
100742 atoms, 102094 bonds, 12124 residues, 27 models selected
> select add #4.35
102084 atoms, 103460 bonds, 12298 residues, 28 models selected
> select add #4.36
103646 atoms, 105040 bonds, 12496 residues, 29 models selected
> select add #4.37
105251 atoms, 106671 bonds, 12703 residues, 30 models selected
> select add #4.38
106593 atoms, 108037 bonds, 12877 residues, 31 models selected
> select add #4.39
108155 atoms, 109617 bonds, 13075 residues, 32 models selected
> select add #4.40
109760 atoms, 111248 bonds, 13282 residues, 33 models selected
> select add #4.41
111102 atoms, 112614 bonds, 13456 residues, 34 models selected
> select add #4.42
112664 atoms, 114194 bonds, 13654 residues, 35 models selected
> select add #4.43
114269 atoms, 115825 bonds, 13861 residues, 36 models selected
> select add #4.44
115611 atoms, 117191 bonds, 14035 residues, 37 models selected
> select add #4.45
117173 atoms, 118771 bonds, 14233 residues, 38 models selected
> select add #4.46
118778 atoms, 120402 bonds, 14440 residues, 39 models selected
> select add #4.47
120120 atoms, 121768 bonds, 14614 residues, 40 models selected
> select add #4.48
121682 atoms, 123348 bonds, 14812 residues, 41 models selected
> select add #4.49
123287 atoms, 124979 bonds, 15019 residues, 42 models selected
> select add #4.51
125395 atoms, 127102 bonds, 15162 residues, 43 models selected
> select add #4.50
126737 atoms, 128468 bonds, 15336 residues, 44 models selected
> select add #4.53
128845 atoms, 130591 bonds, 15479 residues, 45 models selected
> select add #4.52
130953 atoms, 132714 bonds, 15622 residues, 46 models selected
> select add #4.54
133061 atoms, 134837 bonds, 15765 residues, 47 models selected
> select add #4.55
135169 atoms, 136960 bonds, 15908 residues, 48 models selected
> select add #4.56
137277 atoms, 139083 bonds, 16051 residues, 49 models selected
> select add #4.57
139385 atoms, 141206 bonds, 16194 residues, 50 models selected
> select add #4.58
141493 atoms, 143329 bonds, 16337 residues, 51 models selected
> select add #4.59
143601 atoms, 145452 bonds, 16480 residues, 52 models selected
> select add #4.60
145709 atoms, 147575 bonds, 16623 residues, 53 models selected
> select add #4.61
147817 atoms, 149698 bonds, 16766 residues, 54 models selected
> select add #4.62
149925 atoms, 151821 bonds, 16909 residues, 55 models selected
> select add #4.63
152033 atoms, 153944 bonds, 17052 residues, 56 models selected
> select add #4.64
154141 atoms, 156067 bonds, 17195 residues, 57 models selected
> select add #4.65
156249 atoms, 158190 bonds, 17338 residues, 58 models selected
> select add #4.66
158357 atoms, 160313 bonds, 17481 residues, 59 models selected
> select add #4.67
160465 atoms, 162436 bonds, 17624 residues, 60 models selected
===== 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 - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac13,1
Model Number: Z14J000E1LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 28 days, 19 hours, 18 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Q24i-10:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
ASUS PA279:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 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-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 , 6 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash during auto-completion |
comment:2 by , 6 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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