![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#10037 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000200728280 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 390000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 12705,
"osVersion" : {
"train" : "macOS 13.5.2",
"build" : "22G91",
"releaseType" : "User"
},
"captureTime" : "2023-10-20 18:17:36.6971 +0200",
"incident" : "0EAB41C9-2C34-4B2C-AC02-CA0E22E5105E",
"pid" : 63493,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-10-20 09:25:17.9110 +0200",
"procStartAbsTime" : 8654670391904,
"procExitAbsTime" : 9414809454684,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"425C3742-6366-5FA0-9061-8644ADF1B132","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2DFBA48C-D4FB-8182-EBD7-7BE2886EFDA4",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 14,
"sleepWakeUUID" : "602DDE89-FA1D-425F-ADD0-392E58C63900",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140722875334632\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc98ff0000-7ffca8144000 [241.3M] r-x\/r-x SM=COW ...t_id=ba8e6867",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":63493},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140722875334632\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc98ff0000-7ffca8144000 [241.3M] r-x\/r-x SM=COW ...t_id=ba8e6867",
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"faultingThread" : 0,
"threads" : 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"size" : 20480,
"uuid" : "ba973aa3-7e75-3e17-ba66-60209a667b0d",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/graphics\/_graphics.cpython-39-darwin.so",
"name" : "_graphics.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5779046400,
"size" : 454656,
"uuid" : "5a0f30d4-b4ba-316a-8278-78d0c72f5977",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/mmcif\/mmcif.cpython-39-darwin.so",
"name" : "mmcif.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5788008448,
"size" : 446464,
"uuid" : "363f0a7f-8a13-3465-82ee-3a637fe01cc3",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-39-darwin.so",
"name" : "_mmcif.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5780738048,
"size" : 176128,
"uuid" : "5e4388ca-929a-385d-8f7e-4a6c443b3eab",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/pdb\/_pdbio.cpython-39-darwin.so",
"name" : "_pdbio.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5753749504,
"size" : 16384,
"uuid" : "b3a28b9e-f2e7-30be-b15e-275f4f68c91b",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-39-darwin.so",
"name" : "_sw.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5748441088,
"size" : 4096,
"uuid" : "e1f9fc84-3b63-3ab7-b6d9-8a3d7a31082f",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/alignment_algs\/libalign_algs.dylib",
"name" : "libalign_algs.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5772132352,
"size" : 8192,
"uuid" : "a00af8bb-311a-38a4-a412-a0008241ec74",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/dssp\/_dssp.cpython-39-darwin.so",
"name" : "_dssp.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5774229504,
"size" : 28672,
"uuid" : "b3fdf741-e64a-382d-829e-9788a9d976e1",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-39-darwin.so",
"name" : "_nw.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5782966272,
"size" : 212992,
"uuid" : "a8901c91-b274-3218-b439-1b33a3b7923d",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/matplotlib\/backends\/_backend_agg.cpython-39-darwin.so",
"name" : "_backend_agg.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5753835520,
"size" : 40960,
"uuid" : "7cd22409-3ee7-3f06-a313-edcc12328919",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_elementtree.cpython-39-darwin.so",
"name" : "_elementtree.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5771296768,
"size" : 8192,
"uuid" : "9e241d8d-ee83-3dfd-aa89-fd7a71a7d9de",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_multiprocessing.cpython-39-darwin.so",
"name" : "_multiprocessing.cpython-39-darwin.so"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703324090368,
"size" : 237568,
"uuid" : "642737ce-21cf-3d87-a7b6-7eea2c080a7e",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703324327936,
"size" : 49152,
"uuid" : "3a3fa85c-f1fe-336c-bf68-924fc947ade3",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703322939392,
"size" : 557048,
"uuid" : "d5b303ad-54f4-323b-bbe2-2d0f34c45649",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
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"uuid" : "f1798256-c6b5-335c-bbb5-7978acf41deb",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/hld575/Documents/PHD_LAB/230829_AlphaPulldownPEPTIDES/230911.cxs
> format session
opened ChimeraX session
> save
> /Users/hld575/Documents/PHD_LAB/230829_AlphaPulldownPEPTIDES/231020_CMGPeptidesRrm3Pif1.cxs
> close session
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/ranked_0.pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/ranked_1.pdb
Chain information for ranked_1.pdb #2
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/ranked_2.pdb
Chain information for ranked_2.pdb #3
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/ranked_3.pdb
Chain information for ranked_3.pdb #4
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/ranked_4.pdb
Chain information for ranked_4.pdb #5
---
Chain | Description
B | No description available
C | No description available
D | No description available
> select add #1
2137 atoms, 2164 bonds, 276 residues, 1 model selected
> select add #2
4274 atoms, 4328 bonds, 552 residues, 2 models selected
> select add #3
6411 atoms, 6492 bonds, 828 residues, 3 models selected
> select add #4
8548 atoms, 8656 bonds, 1104 residues, 4 models selected
> select add #5
10685 atoms, 10820 bonds, 1380 residues, 5 models selected
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain C (#1) with ranked_1.pdb, chain C (#2),
sequence alignment score = 637.4
RMSD between 108 pruned atom pairs is 0.460 angstroms; (across all 130 pairs:
4.456)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_2.pdb, chain C (#3),
sequence alignment score = 648.2
RMSD between 98 pruned atom pairs is 0.521 angstroms; (across all 130 pairs:
2.418)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_3.pdb, chain C (#4),
sequence alignment score = 648.2
RMSD between 95 pruned atom pairs is 0.382 angstroms; (across all 130 pairs:
22.713)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_4.pdb, chain C (#5),
sequence alignment score = 637.4
RMSD between 101 pruned atom pairs is 0.312 angstroms; (across all 130 pairs:
20.966)
> select clear
> set bgColor white
> select #1/C
995 atoms, 1007 bonds, 130 residues, 1 model selected
> select #*/C
4975 atoms, 5035 bonds, 650 residues, 5 models selected
> color sel forest green
> select #*/D
4880 atoms, 4955 bonds, 630 residues, 5 models selected
> color sel cornflower blue
> select #*/B
830 atoms, 830 bonds, 100 residues, 5 models selected
> color sel red
> select clear
> select #*/C,D
9855 atoms, 9990 bonds, 1280 residues, 5 models selected
> show sel surfaces
> transperancy 20
Unknown command: transperancy 20
> transparency 20
> transparency 30
> hide #!2 models
> show #!2 models
> select clear
> graphics silhouettes true
> lighting flat
> lighting soft
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> interfaces #!1 & ~solvent
2 buried areas: C D 2572, C B 306
> show sel atoms
> sequence chain #1/B
Alignment identifier is 1/B
> select clear
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C
995 atoms, 1007 bonds, 130 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> select clear
> show #!2 models
> hide #!1 models
> interfaces #!2 & ~solvent
1 buried areas: C D 2688
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!5 models
> hide #!4 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> sequence chain #5/C
Alignment identifier is 5/C
> select #5/C:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/C
995 atoms, 1007 bonds, 130 residues, 1 model selected
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> interfaces #!1 & ~solvent
2 buried areas: C D 2572, C B 306
> sequence chain #1/C
Alignment identifier is 1/C
> view sel
> select clear
> save
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/Superposition_1.cxs
> close session
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899
> /ranked_0.pdb"
Chain information for ranked_0.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899
> /ranked_1.pdb"
Chain information for ranked_1.pdb #2
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899
> /ranked_2.pdb"
Chain information for ranked_2.pdb #3
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899
> /ranked_3.pdb"
Chain information for ranked_3.pdb #4
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899
> /ranked_4.pdb"
Chain information for ranked_4.pdb #5
---
Chain | Description
B | No description available
C | No description available
D | No description available
> graphics silhouettes true
> lighting soft
> set bgColor white
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain C (#1) with ranked_1.pdb, chain C (#2),
sequence alignment score = 644.6
RMSD between 111 pruned atom pairs is 0.427 angstroms; (across all 130 pairs:
4.915)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_2.pdb, chain C (#3),
sequence alignment score = 637.4
RMSD between 110 pruned atom pairs is 0.482 angstroms; (across all 130 pairs:
3.326)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_3.pdb, chain C (#4),
sequence alignment score = 645.2
RMSD between 99 pruned atom pairs is 0.592 angstroms; (across all 130 pairs:
3.344)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_4.pdb, chain C (#5),
sequence alignment score = 648.2
RMSD between 103 pruned atom pairs is 0.520 angstroms; (across all 130 pairs:
4.495)
> select #*/B
1550 atoms, 1555 bonds, 200 residues, 5 models selected
> color sel red
> select #*/C
4975 atoms, 5035 bonds, 650 residues, 5 models selected
> color sel forest green
> select #*/D
4880 atoms, 4955 bonds, 630 residues, 5 models selected
> color sel cornflower blue
> select clear
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> interfaces #1 & ~solvent
2 buried areas: C D 2522, D B 395
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #1/C
Alignment identifier is 1/C
> sequence chain #1/D
Alignment identifier is 1/D
> select add #1
2281 atoms, 2309 bonds, 296 residues, 1 model selected
> show sel cartoons
> select clear
> show sel atoms
> select clear
Drag select of 1 atoms, 3 residues
> select clear
> show #2 models
> hide #2 models
> show #3 models
> hide #1 models
Drag select of 13 residues
> select clear
> hide #3 models
> show #3 models
> show #1 models
> hide #3 models
> show #3 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #3 models
> show #2 models
> sequence chain #1/B,D
Chains must have same sequence
> interfaces #2 & ~solvent
2 buried areas: C D 2532, D B 402
> interfaces #2 & ~solvent
2 buried areas: C D 2532, D B 402
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/D
Alignment identifier is 2/D
> hide #2 models
> show #3 models
> interfaces #3 & ~solvent
2 buried areas: C D 2579, C B 571
> select clear
> interfaces #3 & ~solvent
2 buried areas: C D 2579, C B 571
> sequence chain #3/D
Alignment identifier is 3/D
> sequence chain #3/C
Alignment identifier is 3/C
> sequence chain #3/B
Alignment identifier is 3/B
> hide #3 models
> show #4 models
> show #3 models
> hide #3 models
> interfaces #4 & ~solvent
3 buried areas: C D 2656, D B 401, C B 304
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/c
Alignment identifier is 4/C
> sequence chain #4/d
Alignment identifier is 4/D
> hide #4 models
> show #5 models
> interfaces #5 & ~solvent
3 buried areas: C D 2616, C B 447, D B 305
> sequence chain #5/b
Alignment identifier is 5/B
> sequence chain #5/c
Alignment identifier is 5/C
> sequence chain #5/d
Alignment identifier is 5/D
> save
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899
> /Superposition_2.cxs"
> close session
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899
> /ranked_0.pdb"
Chain information for ranked_0.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899
> /ranked_2.pdb"
Chain information for ranked_2.pdb #2
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899
> /ranked_3.pdb"
Chain information for ranked_3.pdb #3
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899
> /ranked_4.pdb"
Chain information for ranked_4.pdb #4
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899
> /ranked_1.pdb"
Chain information for ranked_1.pdb #5
---
Chain | Description
B | No description available
C | No description available
D | No description available
> graphics silhouettes true
> lighting soft
> set bgColor white
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain C (#1) with ranked_2.pdb, chain C (#2),
sequence alignment score = 636.8
RMSD between 97 pruned atom pairs is 0.546 angstroms; (across all 130 pairs:
25.033)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_3.pdb, chain C (#3),
sequence alignment score = 638.6
RMSD between 88 pruned atom pairs is 0.349 angstroms; (across all 130 pairs:
6.007)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_4.pdb, chain C (#4),
sequence alignment score = 644.6
RMSD between 92 pruned atom pairs is 0.421 angstroms; (across all 130 pairs:
5.996)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_1.pdb, chain C (#5),
sequence alignment score = 633.8
RMSD between 96 pruned atom pairs is 0.419 angstroms; (across all 130 pairs:
10.208)
> select #*/B
1600 atoms, 1615 bonds, 190 residues, 5 models selected
> color sel orange red
> color sel red
> select #*/C
4975 atoms, 5035 bonds, 650 residues, 5 models selected
> color sel forest green
> select #*/D
4880 atoms, 4955 bonds, 630 residues, 5 models selected
> color sel cornflower blue
> select clear
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #3 models
> show #3 models
> interfaces ~solvent
82 buried areas: #4/C #3/C 5562, #3/C #5/C 5105, #1/D #2/D 5011, #4/D #1/D
4972, #4/D #3/D 4877, #4/C #1/C 4869, #4/D #2/D 4869, #3/C #1/C 4855, #3/D
#2/D 4770, #4/C #5/C 4710, #1/C #5/C 4691, #1/C #2/C 4664, #3/C #2/C 4602,
#5/C #2/C 4563, #4/C #2/C 4377, #3/D #1/D 4336, #5/D #2/D 3843, #1/D #5/D
3835, #3/D #5/D 3830, #4/D #5/D 3813, #3/C #3/D 2687, #3/C #1/D 2679, #3/C
#5/D 2666, #3/C #4/D 2662, #2/C #5/D 2660, #3/C #2/D 2655, #2/C #3/D 2649,
#2/C #1/D 2640, #4/C #3/D 2639, #4/C #1/D 2634, #5/C #1/D 2627, #5/C #3/D
2627, #2/C #4/D 2625, #4/C #4/D 2622, #2/C #2/D 2622, #5/C #4/D 2615, #4/C
#2/D 2613, #4/C #5/D 2601, #5/C #2/D 2601, #5/C #5/D 2595, #1/C #3/D 2570,
#1/C #1/D 2568, #1/C #4/D 2559, #1/C #2/D 2550, #1/C #5/D 2540, #4/B #5/B
1116, #4/C #4/B 752, #4/B #3/B 734, #1/C #4/B 721, #3/C #4/B 717, #5/C #4/B
709, #2/C #4/B 689, #3/B #2/B 687, #4/C #5/B 682, #3/B #5/B 667, #3/C #5/B
661, #1/C #5/B 652, #5/C #5/B 647, #2/C #5/B 645, #4/D #2/B 599, #1/D #2/B
577, #2/D #2/B 565, #3/D #2/B 530, #4/C #1/B 492, #4/C #3/B 485, #5/C #1/B
477, #2/C #3/B 474, #5/D #2/B 471, #1/C #1/B 461, #1/C #3/B 451, #5/C #3/B
446, #2/C #1/B 445, #3/C #3/B 445, #3/D #4/B 422, #3/C #1/B 409, #4/D #4/B
360, #4/D #3/B 356, #1/D #3/B 335, #3/D #3/B 327, #2/D #3/B 320, #1/B #2/B
320, #1/D #4/B 308
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #1/C
Alignment identifier is 1/C
> sequence chain #1/D
Alignment identifier is 1/D
> sequence chain #12D
Missing or invalid "chains" argument: invalid chains specifier
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> sequence chain #2/D
Alignment identifier is 2/D
> hide #1 models
> show #2 models
> hide #2 models
> sequence chain #3/*
Chains must have same sequence
> sequence chain #3/B
Alignment identifier is 3/B
> sequence chain #3/C
Alignment identifier is 3/C
> sequence chain #3/D
Alignment identifier is 3/D
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/C
Alignment identifier is 4/C
> sequence chain #4/D
Alignment identifier is 4/D
> show #4 models
> hide #4 models
> show #5 models
> sequence chain #5/B
Alignment identifier is 5/B
> sequence chain #5/C
Alignment identifier is 5/C
> sequence chain #5/D
Alignment identifier is 5/D
> save
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899
> /Superposition_3.cxs"
> close session
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/4_Q9UNS1_634-711_and_P04908_and_P06899
> /ranked_0.pdb"
Chain information for ranked_0.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/4_Q9UNS1_634-711_and_P04908_and_P06899
> /ranked_1.pdb"
Chain information for ranked_1.pdb #2
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/4_Q9UNS1_634-711_and_P04908_and_P06899
> /ranked_2.pdb"
Chain information for ranked_2.pdb #3
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/4_Q9UNS1_634-711_and_P04908_and_P06899
> /ranked_3.pdb"
Chain information for ranked_3.pdb #4
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/4_Q9UNS1_634-711_and_P04908_and_P06899
> /ranked_4.pdb"
Chain information for ranked_4.pdb #5
---
Chain | Description
B | No description available
C | No description available
D | No description available
> set bgColor white
> graphics silhouettes true
> lighting soft
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain C (#1) with ranked_1.pdb, chain C (#2),
sequence alignment score = 645.2
RMSD between 101 pruned atom pairs is 0.688 angstroms; (across all 130 pairs:
2.629)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_2.pdb, chain C (#3),
sequence alignment score = 645.2
RMSD between 99 pruned atom pairs is 0.414 angstroms; (across all 130 pairs:
4.625)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_3.pdb, chain C (#4),
sequence alignment score = 641.6
RMSD between 96 pruned atom pairs is 0.550 angstroms; (across all 130 pairs:
3.664)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_4.pdb, chain C (#5),
sequence alignment score = 645.2
RMSD between 96 pruned atom pairs is 0.599 angstroms; (across all 130 pairs:
3.471)
> select #*/B
3200 atoms, 3240 bonds, 390 residues, 5 models selected
> color sel red
> select #*/C
4975 atoms, 5035 bonds, 650 residues, 5 models selected
> color sel forest green
> select #*/D
4880 atoms, 4955 bonds, 630 residues, 5 models selected
> color sel cornflower blue
> select clear
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #5 models
> show #4 models
> show #3 models
> show #2 models
> interfaces ~solvent
95 buried areas: #2/C #4/C 5693, #3/C #4/C 5654, #5/C #4/C 5603, #3/C #2/C
5511, #1/C #2/C 5438, #2/C #5/C 5402, #3/C #5/C 5330, #2/D #5/D 5251, #5/D
#4/D 5195, #1/C #5/C 5134, #1/C #4/C 5031, #1/C #3/C 4947, #2/D #4/D 4871,
#1/D #4/D 4539, #3/D #2/D 4362, #1/D #3/D 4329, #1/D #5/D 4292, #1/D #2/D
4271, #3/D #4/D 4228, #3/D #5/D 4158, #5/C #4/D 2581, #3/C #4/D 2576, #5/C
#2/D 2575, #5/C #3/D 2575, #3/C #3/D 2569, #3/C #2/D 2568, #5/C #5/D 2559,
#5/C #1/D 2556, #3/C #5/D 2555, #3/C #1/D 2547, #2/C #4/D 2545, #2/C #2/D
2539, #2/C #3/D 2538, #4/C #4/D 2537, #4/C #2/D 2534, #1/C #4/D 2532, #4/C
#3/D 2529, #1/C #2/D 2528, #1/C #3/D 2524, #2/C #5/D 2524, #2/C #1/D 2523,
#4/C #5/D 2520, #4/C #1/D 2515, #1/C #5/D 2515, #1/C #1/D 2513, #5/B #4/B
2251, #2/B #4/B 2236, #2/B #5/B 2213, #1/B #3/B 2176, #3/B #2/B 1661, #1/B
#5/B 1373, #1/B #4/B 1360, #3/B #4/B 1306, #1/B #2/B 1145, #2/D #4/B 804, #3/B
#5/B 757, #4/D #4/B 722, #5/D #4/B 717, #3/D #4/B 656, #5/D #3/B 639, #4/D
#3/B 620, #2/D #3/B 609, #1/D #4/B 593, #3/C #5/B 562, #5/C #5/B 561, #2/C
#5/B 545, #4/C #5/B 539, #3/D #3/B 530, #1/C #5/B 515, #5/C #1/B 506, #1/D
#3/B 504, #2/D #5/B 488, #3/D #5/B 483, #5/C #3/B 480, #1/C #1/B 480, #2/C
#1/B 477, #4/D #5/B 474, #5/D #5/B 471, #1/D #5/B 465, #3/C #1/B 458, #4/C
#1/B 450, #2/C #3/B 433, #1/C #3/B 431, #4/C #3/B 428, #2/D #1/B 416, #3/C
#3/B 413, #5/D #1/B 410, #4/D #1/B 397, #1/D #1/B 336, #3/D #1/B 334, #5/C
#4/B 332, #4/C #4/B 325, #3/C #4/B 324, #1/C #4/B 314, #2/C #4/B 310
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> sequence chain #1/B
Alignment identifier is 1/B
> interfaces select & #1 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> interfaces #1 & ~solvent
3 buried areas: C D 2513, C B 480, D B 336
> sequence chain #1/C
Alignment identifier is 1/C
> sequence chain #1/D
Alignment identifier is 1/D
> hide #1 models
> show #2 models
> interfaces #2 & ~solvent
1 buried areas: C D 2539
> hide #2 models
> show #3 models
> interfaces #3 & ~solvent
3 buried areas: C D 2569, D B 530, C B 413
> sequence chain #3/b
Alignment identifier is 3/B
> sequence chain #3/c
Alignment identifier is 3/C
> sequence chain #3/d
Alignment identifier is 3/D
> hide #3 models
> show #4 models
> interfaces #4 & ~solvent
3 buried areas: C D 2537, D B 722, C B 325
> sequence chain #3/d
Alignment identifier is 3/D
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/c
Alignment identifier is 4/C
> sequence chain #4/d
Alignment identifier is 4/D
> hide #4 models
> show #5 models
> interfaces #5 & ~solvent
3 buried areas: C D 2559, C B 561, D B 471
> sequence chain #5/b
Alignment identifier is 5/B
> sequence chain #5/c
Alignment identifier is 5/C
> sequence chain #5/d
Alignment identifier is 5/D
> close session
> open
> "/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899
> /Superposition_3.cxs" format session
opened ChimeraX session
> show #1 models
> interfaces select & #1,5 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> interfaces #1,5 & ~solvent
10 buried areas: #1/C #5/C 4691, #1/D #5/D 3835, #5/C #1/D 2627, #5/C #5/D
2595, #1/C #1/D 2568, #1/C #5/D 2540, #1/C #5/B 652, #5/C #5/B 647, #5/C #1/B
477, #1/C #1/B 461
> hide #5 models
> interfaces #1 & ~solvent
2 buried areas: C D 2568, C B 461
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #1/C
Alignment identifier is 1/C
> sequence chain #1/D
Alignment identifier is 1/D
> hide #1 models
> show #2 models
> interfaces #2 & ~solvent
2 buried areas: C D 2622, D B 565
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> sequence chain #2/D
Alignment identifier is 2/D
> hide #2 models
> show #3 models
> interfaces #3 & ~solvent
3 buried areas: C D 2687, C B 445, D B 327
> sequence chain #3/B
Alignment identifier is 3/B
> sequence chain #3/C
Alignment identifier is 3/C
> sequence chain #3/D
Alignment identifier is 3/D
> hide #3 models
> show #4 models
> interfaces #4 & ~solvent
3 buried areas: C D 2622, C B 752, D B 360
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/C
Alignment identifier is 4/C
> sequence chain #4/D
Alignment identifier is 4/D
> show #5 models
> hide #4 models
> interfaces #5 & ~solvent
2 buried areas: C D 2595, C B 647
> sequence chain #5/B
Alignment identifier is 5/B
> sequence chain #5/C
Alignment identifier is 5/C
> sequence chain #5/D
Alignment identifier is 5/D
> close session
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/ranked_0.pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/ranked_1.pdb
Chain information for ranked_1.pdb #2
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/ranked_2.pdb
Chain information for ranked_2.pdb #3
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/ranked_3.pdb
Chain information for ranked_3.pdb #4
---
Chain | Description
B | No description available
C | No description available
D | No description available
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/ranked_4.pdb
Chain information for ranked_4.pdb #5
---
Chain | Description
B | No description available
C | No description available
D | No description available
> set bgColor white
> graphics silhouettes true
> lighting soft
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain C (#1) with ranked_1.pdb, chain C (#2),
sequence alignment score = 637.4
RMSD between 98 pruned atom pairs is 0.443 angstroms; (across all 130 pairs:
23.512)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_2.pdb, chain C (#3),
sequence alignment score = 645.2
RMSD between 93 pruned atom pairs is 0.320 angstroms; (across all 130 pairs:
20.678)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_3.pdb, chain C (#4),
sequence alignment score = 644.6
RMSD between 108 pruned atom pairs is 0.557 angstroms; (across all 130 pairs:
3.918)
Matchmaker ranked_0.pdb, chain C (#1) with ranked_4.pdb, chain C (#5),
sequence alignment score = 648.2
RMSD between 92 pruned atom pairs is 0.406 angstroms; (across all 130 pairs:
23.947)
> select #*/B
2375 atoms, 2400 bonds, 300 residues, 5 models selected
> color sel red
> select #*/C
4975 atoms, 5035 bonds, 650 residues, 5 models selected
> color sel forest green
> select #*/D
4880 atoms, 4955 bonds, 630 residues, 5 models selected
> color sel cornflower blue
> select clear
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> interfaces #1 & ~solvent
1 buried areas: C D 2533
> show #2 models
> hide #1 models
> interfaces #2 & ~solvent
2 buried areas: C D 2585, D B 460
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> sequence chain #2/D
Alignment identifier is 2/D
> hide #2 models
> show #3 models
> interfaces #3 & ~solvent
2 buried areas: C D 2576, D B 328
> sequence chain #3/B
Alignment identifier is 3/B
> sequence chain #3/D
Alignment identifier is 3/D
> hide #3 models
> show #4 models
> interfaces #4 & ~solvent
2 buried areas: C D 2640, C B 382
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/C
Alignment identifier is 4/C
> hide #4 models
> show #5 models
> interfaces #5 & ~solvent
3 buried areas: C D 2600, C B 677, D B 387
> sequence chain #5/B
Alignment identifier is 5/B
> sequence chain #5/C
Alignment identifier is 5/C
> sequence chain #5/D
Alignment identifier is 5/D
> hide #5 models
> show #2 models
> interfaces #2 & ~solvent
2 buried areas: C D 2585, D B 460
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/D
Alignment identifier is 2/D
> save
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/Superposition_5.cxs
> close session
> open
> /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/Superposition_1.cxs
> format session
opened ChimeraX session
> interfaces #!1 & ~solvent
2 buried areas: C D 2572, C B 306
> show #!2 models
> hide #!1 models
> interfaces #!2 & ~solvent
1 buried areas: C D 2688
> hide #!2 models
> show #!3 models
> interfaces #!3 & ~solvent
1 buried areas: C D 2675
> hide #!3 models
> show #!4 models
> interfaces #!4 & ~solvent
2 buried areas: C D 2612, D B 376
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!5 models
> interfaces #!5 & ~solvent
2 buried areas: C D 2590, C B 360
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11C0001ADK/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 23 days, 21 hours, 8 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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