![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16661 closed defect (can't reproduce)
Crash in ~QAccessibleCache on exit
| 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-15.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 160000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,8",
"coalitionID" : 2508,
"osVersion" : {
"train" : "macOS 15.2",
"build" : "24C101",
"releaseType" : "User"
},
"captureTime" : "2025-01-21 22:37:51.2752 +0800",
"codeSigningMonitor" : 2,
"incident" : "0000AC49-9FB1-406D-A058-FD75761E0FA6",
"pid" : 26273,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-21 22:29:35.2790 +0800",
"procStartAbsTime" : 3837356606261,
"procExitAbsTime" : 3849260149510,
"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":"E573D5CB-EBB2-5219-A0D2-232D0832A6FE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FA6D85C6-97B4-A94A-A50A-5A1D8573717D",
"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" : "35311350-AC8D-4824-B449-A6992143D63D",
"wakeTime" : 4835,
"sleepWakeUUID" : "10BBA22C-CEA8-4DFF-853C-B04D818F7A45",
"sip" : "enabled",
"vmRegionInfo" : "0x772f3324af20 is not in any region. Bytes after previous region: 25489876791073 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 1504K] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000772f3324af20","rawCodes":[1,131044605210400],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000772f3324af20"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":26273},
"vmregioninfo" : "0x772f3324af20 is not in any region. Bytes after previous region: 25489876791073 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 1504K] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
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"name" : "dyld"
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Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"
Log from Tue Jan 21 15:01:50 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"
Log from Mon Jan 20 14:17:30 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"
Log from Mon Jan 20 11:17:03 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/qianyuxia/Tianjin University/Works/Structure/OXGR1
> 结构/LTE4/GPCR_LTE4_J460_20250114_5_real_space_refined.pdb"
Summary of feedback from opening /Users/qianyuxia/Tianjin
University/Works/Structure/OXGR1
结构/LTE4/GPCR_LTE4_J460_20250114_5_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.008 0.070 9136
Ignored bad PDB record found on line 23
ANGLE : 0.960 10.549 12417
Ignored bad PDB record found on line 24
CHIRALITY : 0.056 0.198 1400
17 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 15 15 ILE D 29 LEU D 45
1 17
Start residue of secondary structure not found: HELIX 16 16 GLY D 50 LYS D 61
1 12
Start residue of secondary structure not found: HELIX 17 17 SER D 67 THR D 84
1 18
Start residue of secondary structure not found: HELIX 18 18 ILE D 109 VAL D
134 1 26
Start residue of secondary structure not found: HELIX 19 19 SER D 143 HIS D
145 5 3
8 messages similar to the above omitted
Chain information for GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> open "/Users/qianyuxia/Tianjin University/Works/Structure/OXGR1
> 结构/Apo/GPCR_Apo_State2_20250119_2_real_space_refined.pdb"
Summary of feedback from opening /Users/qianyuxia/Tianjin
University/Works/Structure/OXGR1
结构/Apo/GPCR_Apo_State2_20250119_2_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.007 0.079 9257
Ignored bad PDB record found on line 23
ANGLE : 1.120 14.635 12550
Ignored bad PDB record found on line 24
CHIRALITY : 0.065 0.282 1424
17 messages similar to the above omitted
Chain information for GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide atoms
> show cartoons
> style stick
Changed 18004 atom styles
> set bgColor white
> show ligand
> cartoon style width 1
> transparency 80 ribbons
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | ss
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 GPCR_LTE4_J460_20250114_5_real_space_refined.pdb, chain A (#1) with
GPCR_Apo_State2_20250119_2_real_space_refined.pdb, chain A (#2), sequence
alignment score = 1045.1
RMSD between 228 pruned atom pairs is 0.932 angstroms; (across all 275 pairs:
1.909)
> select #1/C:62
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
57 atoms, 60 bonds, 6 residues, 1 model selected
> select up
2600 atoms, 2647 bonds, 338 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/C:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
48 atoms, 48 bonds, 6 residues, 1 model selected
> select up
2600 atoms, 2647 bonds, 338 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/E:97
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 3 residues, 1 model selected
> select up
925 atoms, 951 bonds, 119 residues, 1 model selected
> select up
1218 atoms, 1247 bonds, 161 residues, 1 model selected
> select up
1799 atoms, 1845 bonds, 235 residues, 1 model selected
> select up
6461 atoms, 6610 bonds, 814 residues, 1 model selected
> select down
1799 atoms, 1845 bonds, 235 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/E:23
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
57 atoms, 56 bonds, 8 residues, 1 model selected
> select up
917 atoms, 943 bonds, 118 residues, 1 model selected
> select up
1000 atoms, 1025 bonds, 131 residues, 1 model selected
> select up
1782 atoms, 1828 bonds, 233 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/D:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
363 atoms, 369 bonds, 53 residues, 1 model selected
> select up
4561 atoms, 4661 bonds, 563 residues, 1 model selected
> select down
363 atoms, 369 bonds, 53 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #2/D:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
72 atoms, 71 bonds, 9 residues, 1 model selected
> select up
403 atoms, 409 bonds, 53 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/B:27
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
207 atoms, 206 bonds, 26 residues, 1 model selected
> select up
402 atoms, 401 bonds, 52 residues, 1 model selected
> select up
412 atoms, 410 bonds, 54 residues, 1 model selected
> select up
1896 atoms, 1929 bonds, 232 residues, 1 model selected
> select up
4198 atoms, 4292 bonds, 510 residues, 1 model selected
> select down
1896 atoms, 1929 bonds, 232 residues, 1 model selected
> color sel #b18aa6ff
> select #2/B:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 12 residues, 1 model selected
> select up
1494 atoms, 1528 bonds, 180 residues, 1 model selected
> select up
1554 atoms, 1587 bonds, 187 residues, 1 model selected
> select up
1896 atoms, 1929 bonds, 232 residues, 1 model selected
> color sel #abd7b8ff
> select #1/A:241
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
2237 atoms, 2299 bonds, 277 residues, 1 model selected
> select up
4198 atoms, 4292 bonds, 510 residues, 1 model selected
> select down
2237 atoms, 2299 bonds, 277 residues, 1 model selected
> color sel #9ab67dff
> select #2/A:215
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
235 atoms, 239 bonds, 31 residues, 1 model selected
> select up
2363 atoms, 2427 bonds, 294 residues, 1 model selected
> color sel #fdadc2ff
> transparency 80 ribbons
> select clear
> select H
35 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 1 residue, 1 model selected
> color sel #b180a6ff
> color sel byhetero
> select sel :< 5
422 atoms, 415 bonds, 45 residues, 2 models selected
> select add #2
4452 atoms, 4546 bonds, 1 pseudobond, 544 residues, 3 models selected
> select subtract #2
193 atoms, 190 bonds, 18 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 193 atom styles
> color sel byhetero
> select clear
> save "/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"
——— End of log from Mon Jan 20 11:17:03 2025 ———
opened ChimeraX session
> select #2/A:87
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #2/A:91
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> select clear
> select #2/A:92
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #2/A:93
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #2/A:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/A:99
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #2/A:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/A:101
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #2/A:105
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/A:106
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #2/A:110
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #2/A:190
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/A:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #2/A:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/A:198
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select clear
> select #2/A:265
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/A:268
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select clear
> select #2/A:84
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
85 atoms, 85 bonds, 11 residues, 1 model selected
> select up
2363 atoms, 2427 bonds, 294 residues, 1 model selected
> select up
4259 atoms, 4356 bonds, 526 residues, 1 model selected
> select up
8422 atoms, 8613 bonds, 1036 residues, 2 models selected
> select up
8422 atoms, 8613 bonds, 1036 residues, 2 models selected
> select up
8422 atoms, 8613 bonds, 1036 residues, 2 models selected
> select up
8422 atoms, 8613 bonds, 1036 residues, 2 models selected
> color sel byhetero
> select clear
> hide #!2 models
> select #1/B:241
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
162 atoms, 162 bonds, 19 residues, 1 model selected
> select up
1494 atoms, 1528 bonds, 180 residues, 1 model selected
> select up
1554 atoms, 1587 bonds, 187 residues, 1 model selected
> select up
1896 atoms, 1929 bonds, 232 residues, 1 model selected
> select ((#1/A & ::polymer_type>0 ) & ((#1/B & ::polymer_type>0 ) :<4)) | ((#1/B & ::polymer_type>0 ) & ((#1/A & ::polymer_type>0 ) :<4))
201 atoms, 190 bonds, 23 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 201 atom styles
> color sel byhetero
> select clear
> show #!2 models
> hide #!1 models
> select #2/B:238
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 12 residues, 1 model selected
> select up
1494 atoms, 1528 bonds, 180 residues, 1 model selected
> select up
1554 atoms, 1587 bonds, 187 residues, 1 model selected
> select up
1896 atoms, 1929 bonds, 232 residues, 1 model selected
> select clear
> select #2/B:238
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 12 residues, 1 model selected
> select up
1494 atoms, 1528 bonds, 180 residues, 1 model selected
> select up
1554 atoms, 1587 bonds, 187 residues, 1 model selected
> select up
1896 atoms, 1929 bonds, 232 residues, 1 model selected
> select ((#2/A & ::polymer_type>0 ) & ((#2/B & ::polymer_type>0 ) :<4)) | ((#2/B & ::polymer_type>0 ) & ((#2/A & ::polymer_type>0 ) :<4))
357 atoms, 342 bonds, 43 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 357 atom styles
> color sel byhetero
> select clear
> show #!1 models
> save "/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"
——— End of log from Mon Jan 20 14:17:30 2025 ———
opened ChimeraX session
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> ui mousemode right distance
> distance #2/A:145@ND1 #2/B:31@NH2
Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A HIS
145 ND1 and /B ARG 31 NH2: 5.289Å
> ~distance #2/A:145@ND1 #2/B:31@NH2
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
96 atoms, 99 bonds, 12 residues, 1 model selected
> select down
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> distance #2/A:145@O #2/B:31@NH2
Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A HIS
145 O and /B ARG 31 NH2: 4.884Å
> ~distance #2/A:145@O #2/B:31@NH2
> distance #2/A:145@N #2/B:31@NH2
Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A HIS
145 N and /B ARG 31 NH2: 5.708Å
> ~distance #2/A:145@N #2/B:31@NH2
> select #2/A:145@CB
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
96 atoms, 99 bonds, 12 residues, 1 model selected
> show sel cartoons
> select clear
> distance #2/A:145@CB #2/B:31@NH2
Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A HIS
145 CB and /B ARG 31 NH2: 4.326Å
> ~distance #2/A:145@CB #2/B:31@NH2
> select #2/A:145@CB
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> distance #2/A:145@C #2/B:31@NH2
Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A HIS
145 C and /B ARG 31 NH2: 4.782Å
> ~distance #2/A:145@C #2/B:31@NH2
> distance #2/B:31@NH2 #2/A:145@CB
Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/B ARG 31
NH2 and /A HIS 145 CB: 4.326Å
> ~distance #2/B:31@NH2 #2/A:145@CB
> select #2/B:238
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 12 residues, 1 model selected
> select up
1494 atoms, 1528 bonds, 180 residues, 1 model selected
> select up
1554 atoms, 1587 bonds, 187 residues, 1 model selected
> select up
1896 atoms, 1929 bonds, 232 residues, 1 model selected
> hide sel atoms
> select #2/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
96 atoms, 99 bonds, 12 residues, 1 model selected
> select up
2363 atoms, 2427 bonds, 294 residues, 1 model selected
> select up
4259 atoms, 4356 bonds, 526 residues, 1 model selected
> select clear
> ui mousemode right "translate selected models"
> show ligand
[Repeated 2 time(s)]
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> select #2/B:238
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 12 residues, 1 model selected
> select up
1494 atoms, 1528 bonds, 180 residues, 1 model selected
> select up
1554 atoms, 1587 bonds, 187 residues, 1 model selected
> select up
1896 atoms, 1929 bonds, 232 residues, 1 model selected
> select ((#2/A & ::polymer_type>0 ) & ((#2/B & ::polymer_type>0 ) :<4)) | ((#2/B & ::polymer_type>0 ) & ((#2/A & ::polymer_type>0 ) :<4))
357 atoms, 342 bonds, 43 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 357 atom styles
> select clear
[Repeated 2 time(s)]
> select #2/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
96 atoms, 99 bonds, 12 residues, 1 model selected
> show sel cartoons
> select #2/B:24
11 atoms, 10 bonds, 1 residue, 1 model selected
> view matrix models
> #2,0.99686,-0.06461,0.045786,-27.436,-0.065497,-0.99769,0.01815,216.05,0.044507,-0.021092,-0.99879,210.8
> show #!1 models
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 GPCR_LTE4_J460_20250114_5_real_space_refined.pdb, chain A (#1) with
GPCR_Apo_State2_20250119_2_real_space_refined.pdb, chain A (#2), sequence
alignment score = 1045.1
RMSD between 228 pruned atom pairs is 0.932 angstroms; (across all 275 pairs:
1.909)
> select clear
> hide #!2 models
> ui mousemode right distance
> distance #1/A:190@OD1 #1/F:1@N30
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A ASP 190
OD1 and /F LIG 1 N30: 3.524Å
> distance #1/A:268@NH1 #1/F:1@O28
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A ARG 268
NH1 and /F LIG 1 O28: 2.318Å
> distance #1/A:268@NH2 #1/F:1@O29
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A ARG 268
NH2 and /F LIG 1 O29: 2.486Å
> distance #1/F:1@O23 #1/A:93@OH
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/F LIG 1
O23 and /A TYR 93 OH: 4.409Å
> ~distance #1/F:1@O23 #1/A:93@OH
> ui mousemode right "translate selected models"
> ui mousemode right distance
> distance #1/A:198@OH #1/F:1@O21
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A TYR 198
OH and /F LIG 1 O21: 4.638Å
> ~distance #1/A:198@OH #1/F:1@O21
> distance #1/A:198@OH #1/F:1@O22
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A TYR 198
OH and /F LIG 1 O22: 5.606Å
> ~distance #1/A:198@OH #1/F:1@O22
> ui mousemode right "translate selected models"
> ui mousemode right distance
> distance #1/A:195@CD1 #1/F:1@O22
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A ILE 195
CD1 and /F LIG 1 O22: 4.601Å
> ~distance #1/A:195@CD1 #1/F:1@O22
> distance #1/A:195@CG2 #1/F:1@O21
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A ILE 195
CG2 and /F LIG 1 O21: 5.171Å
> ~distance #1/A:195@CG2 #1/F:1@O21
> ui mousemode right "translate selected models"
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui mousemode right distance
> distance #1/F:1@O23 #1/A:110@NE
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/F LIG 1
O23 and /A ARG 110 NE: 4.075Å
> ~distance #1/F:1@O23 #1/A:110@NE
> distance #1/F:1@O23 #1/A:110@NH1
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/F LIG 1
O23 and /A ARG 110 NH1: 5.367Å
> ~distance #1/F:1@O23 #1/A:110@NH1
> distance #1/F:1@O23 #1/A:110@NH2
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/F LIG 1
O23 and /A ARG 110 NH2: 6.353Å
> ~distance #1/F:1@O23 #1/A:110@NH2
> ui mousemode right "translate selected models"
> show #!2 models
> hide #!2 models
> ui mousemode right distance
> distance #1/F:1@O23 #1/A:93@OH
Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/F LIG 1
O23 and /A TYR 93 OH: 4.409Å
> ui mousemode right distance
> ~distance #1/F:1@O23 #1/A:93@OH
> ui mousemode right "translate selected models"
> transparency 80 ribbons
> select down
Nothing selected
> show #!2 models
> hide #!1 models
> select #2/B:238
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 12 residues, 1 model selected
> select up
1494 atoms, 1528 bonds, 180 residues, 1 model selected
> select up
1554 atoms, 1587 bonds, 187 residues, 1 model selected
> select up
1896 atoms, 1929 bonds, 232 residues, 1 model selected
> select ((#2/A & ::polymer_type>0 ) & ((#2/B & ::polymer_type>0 ) :<4)) | ((#2/B & ::polymer_type>0 ) & ((#2/A & ::polymer_type>0 ) :<4))
357 atoms, 342 bonds, 43 residues, 1 model selected
> select clear
> select #2/A:142
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel cartoons
> select clear
> ui mousemode right distance
> distance #2/A:142@O #2/B:31@NH2
Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A PHE
142 O and /B ARG 31 NH2: 4.802Å
> select clear
> ~distance #2/A:142@O #2/B:31@NH2
> distance #2/B:31@CB #2/A:142@CB
Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/B ARG 31
CB and /A PHE 142 CB: 5.464Å
> ~distance #2/B:31@CB #2/A:142@CB
> ui mousemode right "translate selected models"
> ui mousemode right distance
> distance #2/A:142@O #2/B:31@NE
Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A PHE
142 O and /B ARG 31 NE: 4.460Å
> distance #2/A:142@O #2/B:31@NH2
Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A PHE
142 O and /B ARG 31 NH2: 4.802Å
> ~distance #2/A:142@O #2/B:31@NH2
> ~distance #2/A:142@O #2/B:31@NE
> ui mousemode right "translate selected models"
> select #2/A:143
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
96 atoms, 99 bonds, 12 residues, 1 model selected
> select up
2363 atoms, 2427 bonds, 294 residues, 1 model selected
> show sel cartoons
> select clear
> show #!1 models
> save "/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"
——— End of log from Tue Jan 21 15:01:50 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4 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: Mac16,8
Model Number: MX2H3CH/A
Chip: Apple M4 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.61.3
OS Loader Version: 11881.61.3
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 9天8小时49分钟
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
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: 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 , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in ~QAccessibleCache on exit |
comment:2 by , 9 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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