![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9103 closed defect (can't reproduce)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| 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-13.2.1-arm64-arm-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 0x00000001dec60140 (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" : 260000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,6",
"coalitionID" : 12132,
"osVersion" : {
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"build" : "22D68",
"releaseType" : "User"
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"captureTime" : "2023-05-31 12:07:13.1370 -0400",
"incident" : "D9229C22-55A7-4041-82E5-4A16F1589CE1",
"pid" : 19908,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-05-23 15:06:27.7941 -0400",
"procStartAbsTime" : 3296891248065,
"procExitAbsTime" : 6306475595686,
"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"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "072F8185-3B57-AAC5-2693-67E3F0E895CF",
"throttleTimeout" : 2147483647,
"sleepWakeUUID" : "74002A5C-F34F-4EF4-B1E3-1E830B13D103",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105558350757864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600138000000-600140000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
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"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
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"arch" : "arm64e",
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"size" : 15777792,
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"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
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"path" : "\/usr\/lib\/system\/libdispatch.dylib",
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"size" : 3358720,
"uuid" : "c68fe2e2-e0f3-3caf-ada3-bcc72fba79d0",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
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"arch" : "arm64",
"base" : 4378460160,
"CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
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"size" : 2555904,
"uuid" : "5ee765c2-b52f-3980-9781-73db1abd2bde",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.11"
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
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"uuid" : "191e84f1-4b95-39c8-b253-1c1ef56c0fa8",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
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},
{
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"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=21.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=21.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 1216K 8 \nCG image 1536K 75 \nColorSync 592K 29 \nCoreAnimation 1312K 61 \nCoreGraphics 48K 3 \nCoreUI image data 5120K 40 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 19.2G 1080 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 856.0M 11 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 624K 39 \nStack 155.9M 40 \nStack Guard 56.0M 1 \nVM_ALLOCATE 563.8M 1675 \nVM_ALLOCATE (reserved) 288.0M 4 reserved VM address space (unallocated)\n__AUTH 1944K 365 \n__AUTH_CONST 25.0M 593 \n__CTF 756 1 \n__DATA 20.0M 731 \n__DATA_CONST 37.9M 741 \n__DATA_DIRTY 1994K 233 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 796.2M 146 \n__OBJC_CONST 4787K 329 \n__OBJC_RO 65.5M 1 \n__OBJC_RW 1988K 1 \n__TEXT 825.8M 761 \ndyld private memory 256K 1 \nmapped file 564.4M 92 \nshared memory 3824K 31 \n=========== ======= ======= \nTOTAL 23.5G 7117 \nTOTAL, minus reserved VM space 22.2G 7117 \n",
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"queue" : "com.apple.main-thread"
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},
"trialInfo" : {
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{
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"factorPackIds" : {
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},
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{
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"experiments" : [
{
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"deploymentId" : 400000024
},
{
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"experimentId" : "64406ba83deb637ac8a04419",
"deploymentId" : 900000005
}
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== 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/brendansheehan/python/7XZX.cif
Summary of feedback from opening /Users/brendansheehan/python/7XZX.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 7XZX.cif #1
---
Chain | Description
N | No description available
> open /Users/brendansheehan/python/7XZX.pdb
7XZX.pdb title:
Cryo-em structure of the nucleosome In complex with P53 DNA-binding domain
[more info...]
Chain information for 7XZX.pdb #2
---
Chain | Description | UniProt
A E | histone H3.1 | H31_HUMAN 1-135
B F | histone H4 | H4_HUMAN 0-102
C G | histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | histone H2B type 1-J | H2B1J_HUMAN -3-122
I | DNA (193-mer) |
J | DNA (193-mer) |
K L M N | cellular tumor antigen P53 | P53_HUMAN 94-293
> sequence chain #2/K#2/L#2/M#2/N
Alignment identifier is 1
> hide #2 models
> hide #1 models
> show #2 models
> color #2 bychain
No model chosen to save relative to
> open /Users/brendansheehan/python/7XZX.cif
Summary of feedback from opening /Users/brendansheehan/python/7XZX.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 7XZX.cif #3
---
Chain | Description
N | No description available
> hide #3 models
> hide #2 models
> show #3 models
> show #1 models
> hide #3 models
> close #3
> close #2
> close
> open /Users/brendansheehan/python/7XZX.cif
Summary of feedback from opening /Users/brendansheehan/python/7XZX.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 7XZX.cif #1
---
Chain | Description
N | No description available
> close
> open /Users/brendansheehan/python/7XZX.pdb format pdb
7XZX.pdb title:
Cryo-em structure of the nucleosome In complex with P53 DNA-binding domain
[more info...]
Chain information for 7XZX.pdb #1
---
Chain | Description | UniProt
A E | histone H3.1 | H31_HUMAN 1-135
B F | histone H4 | H4_HUMAN 0-102
C G | histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | histone H2B type 1-J | H2B1J_HUMAN -3-122
I | DNA (193-mer) |
J | DNA (193-mer) |
K L M N | cellular tumor antigen P53 | P53_HUMAN 94-293
> select 1.A
Expected an objects specifier or a keyword
> select /A
801 atoms, 813 bonds, 97 residues, 1 model selected
> select /K
1555 atoms, 1590 bonds, 198 residues, 1 model selected
> select /K /L
3110 atoms, 3180 bonds, 396 residues, 1 model selected
> select not (/K /L)
Expected an objects specifier or a keyword
> select ~/K
17715 atoms, 18753 bonds, 1698 residues, 1 model selected
> select ~/K/L/M/N
13050 atoms, 13983 bonds, 1104 residues, 1 model selected
> delete ~/K/L/M/N
> save TP53_tetramer.mmCIF format mmcif
> open /Users/brendansheehan/Desktop/TP53_tetramer.mmCIF
Chain information for TP53_tetramer.mmCIF #2
---
Chain | Description
K L M N | cellular tumor antigen P53
> hide #1 models
> close #1
> cd /Users/brendansheehan/python/chimeraX
Current working directory is: /Users/brendansheehan/python/chimeraX
> open /Users/brendansheehan/Desktop/TP53_tetramer.mmCIF
Chain information for TP53_tetramer.mmCIF #1
---
Chain | Description
K L M N | cellular tumor antigen P53
> close
> open /Users/brendansheehan/python/7XZX.pdb format pdb
7XZX.pdb title:
Cryo-em structure of the nucleosome In complex with P53 DNA-binding domain
[more info...]
Chain information for 7XZX.pdb #1
---
Chain | Description | UniProt
A E | histone H3.1 | H31_HUMAN 1-135
B F | histone H4 | H4_HUMAN 0-102
C G | histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | histone H2B type 1-J | H2B1J_HUMAN -3-122
I | DNA (193-mer) |
J | DNA (193-mer) |
K L M N | cellular tumor antigen P53 | P53_HUMAN 94-293
> select /K:94-291
1555 atoms, 1590 bonds, 198 residues, 1 model selected
> select /K:94-291
1555 atoms, 1590 bonds, 198 residues, 1 model selected
> show target m
> log metadata #1
Metadata for 7XZX.pdb #1
---
Title | Cryo-em structure of the nucleosome In complex with P53 DNA-binding
domain
Citation | Structural basis for P53 binding to its nucleosomal targetDNA
sequence. PMID: 36714865
Gene sources | Synthetic construct
Synthetic construct
Experimental method | Electron microscopy
Resolution | 4.53Å
> select /K:94-291
1555 atoms, 1590 bonds, 198 residues, 1 model selected
> sequence chain #1/A#1/E
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain /K /L /M /N
Alignment identifier is 2
> select /K-N:94-150
1736 atoms, 1780 bonds, 228 residues, 1 model selected
> select /K-N:94-150
1736 atoms, 1780 bonds, 228 residues, 1 model selected
> select /K-N:94-150
1736 atoms, 1780 bonds, 228 residues, 1 model selected
> select /K:92
Nothing selected
> select /K:94
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> /K-N:94-96
Unknown command: /K-N:94-96
> select /K-N:94-96
72 atoms, 68 bonds, 12 residues, 1 model selected
> color sel red
> select /BFCGDH
Nothing selected
> select /B/F/C/G/D/H
4445 atoms, 4501 bonds, 567 residues, 1 model selected
> color sel dim gray
> color sel light gray
> color sel dim gray
> select /A/E
1611 atoms, 1635 bonds, 195 residues, 1 model selected
> color sel gray
> color sel light gray
> sequence chain /A/E
Alignment identifier is 1
> select /A:38-59/E:37-59
391 atoms, 399 bonds, 45 residues, 1 model selected
> select /A:38-59/E:37-56
369 atoms, 377 bonds, 42 residues, 1 model selected
> select /A:38-59/E:37-53
339 atoms, 346 bonds, 39 residues, 1 model selected
> open pdb 7w9v
'pdb' has no suffix
> open 7w9v
Summary of feedback from opening 7w9v fetched from pdb
---
warnings | Atom HO5' is not in the residue template for DA /I:-72
Atom HO5' is not in the residue template for DA /J:-72
note | Fetching compressed mmCIF 7w9v from
http://files.rcsb.org/download/7w9v.cif
7w9v title:
Cryo-EM structure of nucleosome in complex with p300 acetyltransferase
catalytic core (complex I) [more info...]
Chain information for 7w9v #2
---
Chain | Description | UniProt
A E | Histone H3.1 | H31_HUMAN 1-135
B F | Histone H4 | H4_HUMAN 0-102
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125
I | DNA (145-MER) |
J | DNA (145-MER) |
K | Histone acetyltransferase p300 | EP300_HUMAN 1035-1519 1581-1720
> align #1 toAtoms #2
Unequal number of atoms to pair, 19270 and 18546
> sequence chain #1/I
Alignment identifier is 1/I
> fitmap #1 toAtoms #2
Expected a keyword
Must specify one map, got 0
> sequence chain #2/I
Alignment identifier is 2/I
> select add #2
18885 atoms, 19816 bonds, 374 pseudobonds, 1631 residues, 4 models selected
> select add #1
37816 atoms, 39813 bonds, 374 pseudobonds, 3488 residues, 4 models selected
> select subtract #1
18546 atoms, 19470 bonds, 374 pseudobonds, 1592 residues, 3 models selected
> select #2
18546 atoms, 19470 bonds, 374 pseudobonds, 1592 residues, 3 models selected
> ui tool show "Fit to Segments"
> mmaker #1 to #2
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 7w9v, chain I (#2) with 7XZX.pdb, chain I (#1), sequence alignment
score = 753.9
RMSD between 109 pruned atom pairs is 1.101 angstroms; (across all 144 pairs:
9.852)
> view sel
> hide #1 models
> show #1 models
> select add #1
37816 atoms, 39813 bonds, 374 pseudobonds, 3488 residues, 4 models selected
> open 6GYR
Summary of feedback from opening 6GYR fetched from pdb
---
notes | Fetching compressed mmCIF 6gyr from
http://files.rcsb.org/download/6gyr.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
Fetching CCD 01K from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/01K/01K.cif
6gyr title:
Transcription factor dimerization activates the p300 acetyltransferase [more
info...]
Chain information for 6gyr #3
---
Chain | Description | UniProt
A B C D | Histone acetyltransferase p300 | EP300_HUMAN 1046-1664
Non-standard residues in 6gyr #3
---
01K —
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl
(3R,20R)-20-carbamoyl-3-hydroxy-2,2-dimethyl-4,8,14,22-tetraoxo-12-thia-5,9,15,21-tetraazatricos-1-yl
dihydrogen diphosphate (Lysine-COENZYME A derivative)
ZN — zinc ion
6gyr mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #1 models
> hide #!2 models
> view sel
>
Incomplete command: sequence
>
Unknown command: sequence #3/A
>
Unknown command: sequence #3
> /A
Unknown command: sequence /A
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #3/B #3/C #3/D
Alignment identifier is 1
> select /A:1520-1580
463 atoms, 464 bonds, 29 residues, 1 model selected
> select /A/B/C/D:1520-1580
34168 atoms, 34598 bonds, 34 pseudobonds, 2356 residues, 5 models selected
> select /A:1520-1580
463 atoms, 464 bonds, 29 residues, 1 model selected
> select /A:1520-1580/B:1520-1580
840 atoms, 841 bonds, 1 pseudobond, 53 residues, 2 models selected
> select /A:1520-1580/B:1520-1580/C:1520-1580
1123 atoms, 1122 bonds, 2 pseudobonds, 70 residues, 2 models selected
> select /A:1520-1580/B:1520-1580/C:1520-1580/D:1520-1580
1521 atoms, 1520 bonds, 3 pseudobonds, 95 residues, 2 models selected
> open 6GYT
Summary of feedback from opening 6GYT fetched from pdb
---
notes | Fetching compressed mmCIF 6gyt from
http://files.rcsb.org/download/6gyt.cif
Fetching CCD ALY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/ALY/ALY.cif
6gyt title:
Transcription factor dimerization activates the p300 acetyltransferase [more
info...]
Chain information for 6gyt #4
---
Chain | Description | UniProt
A | Histone acetyltransferase p300 | EP300_HUMAN 1047-1168
B | Histone acetyltransferase p300 | EP300_HUMAN 1047-1168
C | Histone H4 |
Non-standard residues in 6gyt #4
---
ZN — zinc ion
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/C
Alignment identifier is 4/C
> select #4/C:9-10
25 atoms, 24 bonds, 2 residues, 1 model selected
> select #4/C
116 atoms, 115 bonds, 9 residues, 1 model selected
> zoom 2
moved plane near 284.7246646041093 [0.4113376 0.64802213 0.6409904 ]
moved plane far 284.7246646041093 [0.4113376 0.64802213 0.6409904 ]
> select #4/A:1098-1099
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #4/A:1098-1157
1021 atoms, 1035 bonds, 60 residues, 1 model selected
> select #4/B:1103-1104
46 atoms, 45 bonds, 2 residues, 1 model selected
> select #4/B:1069-1103
558 atoms, 566 bonds, 35 residues, 1 model selected
> select
> #4/B:1050-1067,1072-1076,1080-1085,1088-1093,1098-1109,1113-1132,1136-1160,1256-1260,1272-1282
1765 atoms, 1778 bonds, 108 residues, 1 model selected
> select #4/A
2655 atoms, 2670 bonds, 8 pseudobonds, 182 residues, 2 models selected
> color (#!4 & sel) orange
> select #4/B
2741 atoms, 2758 bonds, 8 pseudobonds, 187 residues, 2 models selected
> zoom 1
moved plane near -0.0 [ 0.97322543 -0.11669096 0.19802899]
moved plane far -0.0 [ 0.97322543 -0.11669096 0.19802899]
> zoom .5
moved plane near -284.72465920292035 [ 0.97322543 -0.11669096 0.19802899]
moved plane far -284.72465920292035 [ 0.97322543 -0.11669096 0.19802899]
> select /A:1532-1567/B:1532-1567/C:1532-1567/D:1532-1567
132 atoms, 128 bonds, 10 residues, 1 model selected
> hide #!3 models
> hide #!4 models
> show #1 models
> show #!2 models
> zoom 1.5
moved plane near 284.2313501240269 [ 0.89736995 -0.14949485 0.41518483]
moved plane far 284.2313501240269 [ 0.89736995 -0.14949485 0.41518483]
> open
> /Users/brendansheehan/python/alphafold/output/output/TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
> /Users/brendansheehan/python/alphafold/output/output/TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
> /Users/brendansheehan/python/alphafold/output/output/TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb
> /Users/brendansheehan/python/alphafold/output/output/TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
> /Users/brendansheehan/python/alphafold/output/output/TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #5
---
Chain | Description
A B C D | No description available
Chain information for
TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb #6
---
Chain | Description
A B C D | No description available
Chain information for
TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb #7
---
Chain | Description
A B C D | No description available
Chain information for
TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb #8
---
Chain | Description
A B C D | No description available
Chain information for
TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb #9
---
Chain | Description
A B C D | No description available
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> mmaker #1 #5-9
> matchmaker #1 #5-9
Missing required "to" argument
> mmaker #5-9 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 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#5), sequence alignment score = 1029.7
RMSD between 195 pruned atom pairs is 0.283 angstroms; (across all 198 pairs:
0.438)
Matchmaker 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#6), sequence alignment score = 1029.7
RMSD between 195 pruned atom pairs is 0.258 angstroms; (across all 198 pairs:
0.405)
Matchmaker 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#7), sequence alignment score = 1026.7
RMSD between 194 pruned atom pairs is 0.263 angstroms; (across all 198 pairs:
0.461)
Matchmaker 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain C (#8), sequence alignment score = 1029.7
RMSD between 194 pruned atom pairs is 0.320 angstroms; (across all 198 pairs:
0.517)
Matchmaker 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#9), sequence alignment score = 1029.7
RMSD between 195 pruned atom pairs is 0.311 angstroms; (across all 198 pairs:
0.461)
> hide #1 models
> select #1/M
1555 atoms, 1590 bonds, 198 residues, 1 model selected
> show #1 models
> zoom 1.5
moved plane near 189.487126266606 [0.35405918 0.90229304 0.24598646]
moved plane far 189.487126266606 [0.35405918 0.90229304 0.24598646]
> cofr sel
> hide #1 models
> show #1 models
> mmaker #5-9 to #1/K-N
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 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#5), sequence alignment score = 1029.7
RMSD between 195 pruned atom pairs is 0.283 angstroms; (across all 198 pairs:
0.438)
Matchmaker 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#6), sequence alignment score = 1029.7
RMSD between 195 pruned atom pairs is 0.258 angstroms; (across all 198 pairs:
0.405)
Matchmaker 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#7), sequence alignment score = 1026.7
RMSD between 194 pruned atom pairs is 0.263 angstroms; (across all 198 pairs:
0.461)
Matchmaker 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain C (#8), sequence alignment score = 1029.7
RMSD between 194 pruned atom pairs is 0.320 angstroms; (across all 198 pairs:
0.517)
Matchmaker 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#9), sequence alignment score = 1029.7
RMSD between 195 pruned atom pairs is 0.311 angstroms; (across all 198 pairs:
0.461)
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #1 models
> show #1 models
> hide #1/K-N
> show #1/K-N
> show #6 models
> hide #5 models
> hide #6 models
> show #7 models
> show #8 models
> hide #7 models
> hide #8 models
> show #9 models
> hide #9 models
> show #5 models
> mmaker #5/A to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#5), sequence alignment score = 1026.7
RMSD between 198 pruned atom pairs is 0.268 angstroms; (across all 198 pairs:
0.268)
> mmaker #5/B to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain B (#5), sequence alignment score = 1012.3
RMSD between 198 pruned atom pairs is 0.250 angstroms; (across all 198 pairs:
0.250)
> view sel
> zoom .9
moved plane near -29.30161236175836 [0.79571606 0.23004343 0.56028203]
moved plane far -29.30161236175836 [0.79571606 0.23004343 0.56028203]
> zoom .9
moved plane near -32.55734700229572 [0.79571606 0.23004343 0.56028203]
moved plane far -32.55734700229572 [0.79571606 0.23004343 0.56028203]
> zoom .9
moved plane near -36.17482992885669 [0.79571606 0.23004343 0.56028203]
moved plane far -36.17482992885669 [0.79571606 0.23004343 0.56028203]
> zoom .9
moved plane near -40.19425539462508 [0.79571606 0.23004343 0.56028203]
moved plane far -40.19425539462508 [0.79571606 0.23004343 0.56028203]
> zoom .9
moved plane near -44.66028368082526 [0.79571606 0.23004343 0.56028203]
moved plane far -44.66028368082526 [0.79571606 0.23004343 0.56028203]
> hide #1 models
> show #1 models
> hide #1/K-N
> hide #!2 models
> show #!2 models
> list chains
Unknown command: list chains
> list chains #2
Unknown command: list chains #2
> list
Unknown command: list
> log metadata
Metadata for 7XZX.pdb #1
---
Title | Cryo-em structure of the nucleosome In complex with P53 DNA-binding
domain
Citation | Structural basis for P53 binding to its nucleosomal targetDNA
sequence. PMID: 36714865
Gene sources | Synthetic construct
Synthetic construct
Experimental method | Electron microscopy
Resolution | 4.53Å
Metadata for 7w9v #2
---
Title | Cryo-EM structure of nucleosome in complex with p300 acetyltransferase
catalytic core (complex I)
Citation | Hatazawa, S., Liu, J., Takizawa, Y., Zandian, M., Negishi, L.,
Kutateladze, T.G., Kurumizaka, H. (2022). Structural basis for binding
diversity of acetyltransferase p300 to the nucleosome. Iscience, 25,
104563-104563. PMID: 35754730. DOI: 10.1016/j.isci.2022.104563
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 32373 — open map
Experimental method | Electron microscopy
Resolution | 3.95Å
Metadata for 6gyr #3
---
Title | Transcription factor dimerization activates the p300 acetyltransferase
Citation | Ortega, E., Rengachari, S., Ibrahim, Z., Hoghoughi, N., Gaucher,
J., Holehouse, A.S., Khochbin, S., Panne, D. (2018). Transcription factor
dimerization activates the p300 acetyltransferase. Nature, 562, 538-544. PMID:
30323286. DOI: 10.1038/s41586-018-0621-1
Non-standard residues | 01K —
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl
(3R,20R)-20-carbamoyl-3-hydroxy-2,2-dimethyl-4,8,14,22-tetraoxo-12-thia-5,9,15,21-tetraazatricos-1-yl
dihydrogen diphosphate (Lysine-COENZYME A derivative)
ZN — zinc ion
Gene source | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 3.1Å
Metadata for 6gyt #4
---
Title | Transcription factor dimerization activates the p300 acetyltransferase
Citation | Ortega, E., Rengachari, S., Ibrahim, Z., Hoghoughi, N., Gaucher,
J., Holehouse, A.S., Khochbin, S., Panne, D. (2018). Transcription factor
dimerization activates the p300 acetyltransferase. Nature, 562, 538-544. PMID:
30323286. DOI: 10.1038/s41586-018-0621-1
Non-standard residue | ZN — zinc ion
Gene sources | Xenopus laevis (african clawed frog)
Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.5Å
> sym
Missing or invalid "structures" argument: empty atom specifier
> sym #2
7w9v mmCIF Assemblies
---
1| author_defined_assembly| 1 copy of chain A-K
> sym #2 assembly 1
Made 1 copies for 7w9v assembly 1
> view
> log chains
Chain information for 7XZX.pdb #1
---
Chain | Description | UniProt
A E | histone H3.1 | H31_HUMAN 1-135
B F | histone H4 | H4_HUMAN 0-102
C G | histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | histone H2B type 1-J | H2B1J_HUMAN -3-122
I | DNA (193-mer) |
J | DNA (193-mer) |
K L M N | cellular tumor antigen P53 | P53_HUMAN 94-293
Chain information for 7w9v #2
---
Chain | Description | UniProt
A E | Histone H3.1 | H31_HUMAN 1-135
B F | Histone H4 | H4_HUMAN 0-102
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125
I | DNA (145-MER) |
J | DNA (145-MER) |
K | Histone acetyltransferase p300 | EP300_HUMAN 1035-1519 1581-1720
Chain information for 6gyr #3
---
Chain | Description | UniProt
A B C D | Histone acetyltransferase p300 | EP300_HUMAN 1046-1664
Chain information for 6gyt #4
---
Chain | Description | UniProt
A | Histone acetyltransferase p300 | EP300_HUMAN 1047-1168
B | Histone acetyltransferase p300 | EP300_HUMAN 1047-1168
C | Histone H4 |
Chain information for
TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #5
---
Chain | Description
A B C D | No description available
Chain information for
TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb #6
---
Chain | Description
A B C D | No description available
Chain information for
TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb #7
---
Chain | Description
A B C D | No description available
Chain information for
TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb #8
---
Chain | Description
A B C D | No description available
Chain information for
TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb #9
---
Chain | Description
A B C D | No description available
Chain information for 7w9v #10.1
---
Chain | Description | UniProt
A E | Histone H3.1 | H31_HUMAN 1-135
B F | Histone H4 | H4_HUMAN 0-102
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125
I | DNA (145-MER) |
J | DNA (145-MER) |
K | Histone acetyltransferase p300 | EP300_HUMAN 1035-1519 1581-1720
> hide #!10 models
> hide #!10.1 models
> show #!2 models
> select add #2
20101 atoms, 21060 bonds, 374 pseudobonds, 1790 residues, 4 models selected
> select subtract #2
1555 atoms, 1590 bonds, 198 residues, 1 model selected
> select #2~/K
Expected an objects specifier or a keyword
> select #2
18546 atoms, 19470 bonds, 374 pseudobonds, 1592 residues, 3 models selected
> select #2/A-J
14034 atoms, 14836 bonds, 372 pseudobonds, 1041 residues, 2 models selected
> hide #2/A-J
> select #5/A
6036 atoms, 6120 bonds, 393 residues, 1 model selected
> select #5/A:1-95
1380 atoms, 1409 bonds, 95 residues, 1 model selected
> select clear
> undo
> select #5/A-D:1-95
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> hide #5 models
> show #6 models
> show #5 models
> hide #6 models
> show #6 models
> mmaker #6 to #1/K-N
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 7XZX.pdb, chain M (#1) with
TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#6), sequence alignment score = 1029.7
RMSD between 195 pruned atom pairs is 0.258 angstroms; (across all 198 pairs:
0.405)
> hide #1 models
> show #1 models
> select up
6356 atoms, 6488 bonds, 436 residues, 1 model selected
> select up
24144 atoms, 24480 bonds, 1572 residues, 1 model selected
> select up
202239 atoms, 206444 bonds, 14074 residues, 10 models selected
> select up
202239 atoms, 206444 bonds, 14074 residues, 10 models selected
> select up
202239 atoms, 206444 bonds, 14074 residues, 10 models selected
> select up
202239 atoms, 206444 bonds, 14074 residues, 10 models selected
> select up
202239 atoms, 206444 bonds, 14074 residues, 10 models selected
> select down
24144 atoms, 24480 bonds, 1572 residues, 1 model selected
> select down
6356 atoms, 6488 bonds, 436 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> select down
5520 atoms, 5636 bonds, 380 residues, 1 model selected
> show #1/K-N
> select up
6356 atoms, 6488 bonds, 436 residues, 1 model selected
> mmaker #6/B to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#6), sequence alignment score = 1026.7
RMSD between 198 pruned atom pairs is 0.252 angstroms; (across all 198 pairs:
0.252)
> mmaker #6/A to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#6), sequence alignment score = 1012.3
RMSD between 198 pruned atom pairs is 0.232 angstroms; (across all 198 pairs:
0.232)
> hide #5 models
> hide #6 models
> show #7 models
> mmaker #7/A to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain A (#7), sequence alignment score = 1012.3
RMSD between 198 pruned atom pairs is 0.269 angstroms; (across all 198 pairs:
0.269)
> hide #7 models
> show #8 models
> mmaker #8/A to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#8), sequence alignment score = 1009.3
RMSD between 198 pruned atom pairs is 0.334 angstroms; (across all 198 pairs:
0.334)
> mmaker #8/B to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#8), sequence alignment score = 1021.3
RMSD between 198 pruned atom pairs is 0.329 angstroms; (across all 198 pairs:
0.329)
> show #9 models
> hide #8 models
> mmaker #8/B to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#8), sequence alignment score = 1021.3
RMSD between 198 pruned atom pairs is 0.329 angstroms; (across all 198 pairs:
0.329)
> mmaker #8/A to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#8), sequence alignment score = 1009.3
RMSD between 198 pruned atom pairs is 0.334 angstroms; (across all 198 pairs:
0.334)
> show #8 models
> mmaker #8/B to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#8), sequence alignment score = 1021.3
RMSD between 198 pruned atom pairs is 0.329 angstroms; (across all 198 pairs:
0.329)
> hide #8 models
> mmaker #9/B to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#9), sequence alignment score = 1026.7
RMSD between 198 pruned atom pairs is 0.279 angstroms; (across all 198 pairs:
0.279)
> mmaker #9/A to #1/K
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 7XZX.pdb, chain K (#1) with
TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#9), sequence alignment score = 1012.3
RMSD between 198 pruned atom pairs is 0.282 angstroms; (across all 198 pairs:
0.282)
> hide #1/K-N
> hide #9 models
> close #10
> show #5 models
> select #5/A
6036 atoms, 6120 bonds, 393 residues, 1 model selected
> select #5/A-B
12072 atoms, 12240 bonds, 786 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A #5/B #5/C #5/D #6/A #6/B #6/C #6/D #7/A #7/B #7/C #7/D
> #8/A #8/B #8/C #8/D #9/A #9/B #9/C #9/D
Alignment identifier is 1
> select #5/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #6/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #7/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #8/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #9/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
20400 atoms, 20500 bonds, 1240 residues, 5 models selected
> interfaces select #5/A contacting #5/B
37 contacting residues
> color sel red
> select
> #5/A-D:110-113,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274,327-333
> #6/A-D:110-113,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274,327-333
> #7/A-D:110-113,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274,327-333
> #8/A-D:110-113,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274,327-333
> #9/A-D:110-113,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274,327-333
24640 atoms, 24720 bonds, 1440 residues, 5 models selected
> interfaces select #5/A contacting #5/B
37 contacting residues
> interfaces select #5/A contacting #5/C
18 contacting residues
> hide #5 models
> show #1
> show #5 models
> open /Users/brendansheehan/screenshots/scripts/get_last_shot.py
Traceback (most recent call last):
File "/Users/brendansheehan/screenshots/scripts/get_last_shot.py", line 7, in
files_ = os.listdir(d)
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/bsheehan/screenshots/'
Failed opening file
/Users/brendansheehan/screenshots/scripts/get_last_shot.py:
Error opening python file
/Users/brendansheehan/screenshots/scripts/get_last_shot.py
> open /Users/brendansheehan/screenshots/scripts/get_last_shot.py
Traceback (most recent call last):
File "/Users/brendansheehan/screenshots/scripts/get_last_shot.py", line 7, in
files_ = os.listdir(d)
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/bsheehan/screenshots/'
Failed opening file
/Users/brendansheehan/screenshots/scripts/get_last_shot.py:
Error opening python file
/Users/brendansheehan/screenshots/scripts/get_last_shot.py
> open /Users/brendansheehan/screenshots/scripts/png_to_txt.py
Traceback (most recent call last):
File "/Users/brendansheehan/screenshots/scripts/png_to_txt.py", line 24, in
files_ = os.listdir(d)
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/bsheehan/screenshots/'
Failed opening file /Users/brendansheehan/screenshots/scripts/png_to_txt.py:
Error opening python file
/Users/brendansheehan/screenshots/scripts/png_to_txt.py
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A #5/B #5/C #5/D #6/A #6/B #6/C #6/D #7/A #7/B #7/C #7/D
> #8/A #8/B #8/C #8/D #9/A #9/B #9/C #9/D
Alignment identifier is 2
> select #5/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #6/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #7/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #8/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #9/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
20400 atoms, 20500 bonds, 1240 residues, 5 models selected
> select #5/A-D:333
96 atoms, 92 bonds, 4 residues, 1 model selected
> color sel red
> style sel stick
Changed 96 atom styles
> style sel sphere
Changed 96 atom styles
> show (sel-residues & sidechain) target ab
> select #5/A-D:335
96 atoms, 92 bonds, 4 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> select #5/A-D:333
96 atoms, 92 bonds, 4 residues, 1 model selected
> surface hidePatches sel
> style sel stick
Changed 96 atom styles
> select #5/A-D:337
96 atoms, 92 bonds, 4 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> select #5/A-D:333
96 atoms, 92 bonds, 4 residues, 1 model selected
> color sel red
> select #5/A-D:335
96 atoms, 92 bonds, 4 residues, 1 model selected
> color sel yellow
> select #5/A-D:337
96 atoms, 92 bonds, 4 residues, 1 model selected
> color sel blue
> view sel
> interfaces select #5/A-C contacting #5/D:337
0 contacting residues
> select #5/D:337 : select #5/D:337 : select #5/D:337 : color (#5 & sel) lime
> undo
> select #5/D:337 : select #5/D:337 : select #5/D:337 : color sel lime
> show (sel-residues & sidechain) target ab
> select #5/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #6/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #7/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #8/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
> #9/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357
20400 atoms, 20500 bonds, 1240 residues, 5 models selected
> select #5/A-D:299-318
1152 atoms, 1168 bonds, 80 residues, 1 model selected
> select up
2046 atoms, 2078 bonds, 137 residues, 1 model selected
> select #5/D:333 : show (sel-residues & sidechain) target ab
> color sel lime
> select #5/D:335 : color sel lime
> select #5/D:335 : select #5/D:333 : select #5/D:333 : select #5/D:335 : select #5/D:337 : select #5/D:337 : select #5/D:337 : select #5/D:337 : select #5/D:333 : select #5/D:333 : select #5/D:333 : select #5/D:333 : select #5/D:333 : select #5/A-C:326
45 atoms, 42 bonds, 3 residues, 1 model selected
> select #5/A-D:326
60 atoms, 56 bonds, 4 residues, 1 model selected
> color sel magenta
> show (sel-residues & sidechain) target ab
> select #5/A-D:335
96 atoms, 92 bonds, 4 residues, 1 model selected
> select #5/A-D:3345
Nothing selected
> select #5/A-D:345
56 atoms, 52 bonds, 4 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> select #5/A-D:349
60 atoms, 56 bonds, 4 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> open 2J0Z
Summary of feedback from opening 2J0Z fetched from pdb
---
note | Fetching compressed mmCIF 2j0z from
http://files.rcsb.org/download/2j0z.cif
2j0z title:
p53 tetramerization domain wild type [more info...]
Chain information for 2j0z
---
Chain | Description | UniProt
10.1/A 10.2/A 10.3/A 10.4/A 10.5/A 10.6/A 10.7/A 10.8/A 10.9/A 10.10/A 10.11/A
10.12/A 10.13/A 10.14/A 10.15/A 10.16/A 10.17/A 10.18/A 10.19/A 10.20/A
10.21/A 10.22/A 10.23/A 10.24/A 10.25/A 10.26/A 10.27/A 10.28/A 10.29/A
10.30/A 10.1/B 10.2/B 10.3/B 10.4/B 10.5/B 10.6/B 10.7/B 10.8/B 10.9/B 10.10/B
10.11/B 10.12/B 10.13/B 10.14/B 10.15/B 10.16/B 10.17/B 10.18/B 10.19/B
10.20/B 10.21/B 10.22/B 10.23/B 10.24/B 10.25/B 10.26/B 10.27/B 10.28/B
10.29/B 10.30/B 10.1/C 10.2/C 10.3/C 10.4/C 10.5/C 10.6/C 10.7/C 10.8/C 10.9/C
10.10/C 10.11/C 10.12/C 10.13/C 10.14/C 10.15/C 10.16/C 10.17/C 10.18/C
10.19/C 10.20/C 10.21/C 10.22/C 10.23/C 10.24/C 10.25/C 10.26/C 10.27/C
10.28/C 10.29/C 10.30/C 10.1/D 10.2/D 10.3/D 10.4/D 10.5/D 10.6/D 10.7/D
10.8/D 10.9/D 10.10/D 10.11/D 10.12/D 10.13/D 10.14/D 10.15/D 10.16/D 10.17/D
10.18/D 10.19/D 10.20/D 10.21/D 10.22/D 10.23/D 10.24/D 10.25/D 10.26/D
10.27/D 10.28/D 10.29/D 10.30/D | CELLULAR TUMOR ANTIGEN P53 | P53_HUMAN
326-356
> hide #!2 models
> hide #5 models
> hide #!10 models
> show #!10 models
> hide #1 models
> view sel
> select #10
62640 atoms, 63000 bonds, 3720 residues, 31 models selected
> view sel
> ui tool show "Show Sequence Viewer"
> sequence chain #10.1/A #10.1/B #10.1/C #10.1/D #10.2/A #10.2/B #10.2/C
> #10.2/D #10.3/A #10.3/B #10.3/C #10.3/D #10.4/A #10.4/B #10.4/C #10.4/D
> #10.5/A #10.5/B #10.5/C #10.5/D #10.6/A #10.6/B #10.6/C #10.6/D #10.7/A
> #10.7/B #10.7/C #10.7/D #10.8/A #10.8/B #10.8/C #10.8/D #10.9/A #10.9/B
> #10.9/C #10.9/D #10.10/A #10.10/B #10.10/C #10.10/D #10.11/A #10.11/B
> #10.11/C #10.11/D #10.12/A #10.12/B #10.12/C #10.12/D #10.13/A #10.13/B
> #10.13/C #10.13/D #10.14/A #10.14/B #10.14/C #10.14/D #10.15/A #10.15/B
> #10.15/C #10.15/D #10.16/A #10.16/B #10.16/C #10.16/D #10.17/A #10.17/B
> #10.17/C #10.17/D #10.18/A #10.18/B #10.18/C #10.18/D #10.19/A #10.19/B
> #10.19/C #10.19/D #10.20/A #10.20/B #10.20/C #10.20/D #10.21/A #10.21/B
> #10.21/C #10.21/D #10.22/A #10.22/B #10.22/C #10.22/D #10.23/A #10.23/B
> #10.23/C #10.23/D #10.24/A #10.24/B #10.24/C #10.24/D #10.25/A #10.25/B
> #10.25/C #10.25/D #10.26/A #10.26/B #10.26/C #10.26/D #10.27/A #10.27/B
> #10.27/C #10.27/D #10.28/A #10.28/B #10.28/C #10.28/D #10.29/A #10.29/B
> #10.29/C #10.29/D #10.30/A #10.30/B #10.30/C #10.30/D
Alignment identifier is 3
> select #10/A-D/326E
62640 atoms, 63000 bonds, 3720 residues, 30 models selected
> select #10/A-D:327
2520 atoms, 2520 bonds, 120 residues, 30 models selected
> show (sel-residues & sidechain) target ab
> select #10/A-D/326
62640 atoms, 63000 bonds, 3720 residues, 30 models selected
> select #10/A-D:326
2040 atoms, 1920 bonds, 120 residues, 30 models selected
> show (sel-residues & sidechain) target ab
> select #10/A-D:333
2880 atoms, 2760 bonds, 120 residues, 30 models selected
> show (sel-residues & sidechain) target ab
> select #10/A-D:335
2880 atoms, 2760 bonds, 120 residues, 30 models selected
> show sel target ab
> select #10/A-D:352
1440 atoms, 1320 bonds, 120 residues, 30 models selected
> show sel target ab
> select #10/A-D:337
2880 atoms, 2760 bonds, 120 residues, 30 models selected
> show (sel-residues & sidechain) target ab
> select #10/A-D:349
1800 atoms, 1680 bonds, 120 residues, 30 models selected
> show (sel-residues & sidechain) target ab
> select #10/A-D:349,352
3240 atoms, 3000 bonds, 240 residues, 30 models selected
> select #10/A-D:349,352,333
6120 atoms, 5760 bonds, 360 residues, 30 models selected
> select #10/A-D:349,352,335
6120 atoms, 5760 bonds, 360 residues, 30 models selected
> select #10/A-D:349,352,337
6120 atoms, 5760 bonds, 360 residues, 30 models selected
> select #10/A-D:349,352,335
6120 atoms, 5760 bonds, 360 residues, 30 models selected
> select #10/A-D:345
1680 atoms, 1560 bonds, 120 residues, 30 models selected
> show (sel-residues & sidechain) target ab
> select #10/A-D:345,333
4560 atoms, 4320 bonds, 240 residues, 30 models selected
> select #10/A-D:345,337
4560 atoms, 4320 bonds, 240 residues, 30 models selected
> select #10/A-D:345,337,333
7440 atoms, 7080 bonds, 360 residues, 30 models selected
> select #10/A-D:345,337,33
4560 atoms, 4320 bonds, 240 residues, 30 models selected
> select #10/A-D:345,337,349
6360 atoms, 6000 bonds, 360 residues, 30 models selected
> sell
Unknown command: sell
> select
264879 atoms, 269444 bonds, 436 pseudobonds, 17794 residues, 45 models
selected
> select #1
19270 atoms, 20343 bonds, 1896 residues, 1 model selected
> hide #!10 models
> show #1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select #1
19270 atoms, 20343 bonds, 1896 residues, 1 model selected
> view sel
> show #!2 models
> show #5 models
> hide #5 models
> open
> /Users/brendansheehan/python/alphafold/TERF2_dimer/output/TERF2_dimer_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
TERF2_dimer_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #11
---
Chain | Description
A B | No description available
> open
> /Users/brendansheehan/python/alphafold/TERF2_dimer/output/TERF2_dimer_relaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
TERF2_dimer_relaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb #12
---
Chain | Description
A B | No description available
> open
> /Users/brendansheehan/python/alphafold/TERF2_dimer/output/TERF2_dimer_relaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
TERF2_dimer_relaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb #13
---
Chain | Description
A B | No description available
> open
> /Users/brendansheehan/python/alphafold/TERF2_dimer/output/TERF2_dimer_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
TERF2_dimer_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #14
---
Chain | Description
A B | No description available
> hide #11 models
> show #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> view sel
> hide #1 models
> hide #!2 models
> select subtract #1
Nothing selected
> select add #11
16780 atoms, 16930 bonds, 1084 residues, 1 model selected
No model chosen to save relative to
> hide #11 models
> select subtract #11
Nothing selected
> show #1 models
> show #!2 models
> show #5 models
> select add #5
24144 atoms, 24480 bonds, 1572 residues, 1 model selected
> view sel
> hide #!2 models
> show #!2 models
> select #1/K-N
6220 atoms, 6360 bonds, 792 residues, 1 model selected
> hide #1/K-N
> show #1/K-N
> hide #5 models
Unsupported scale factor (0.000000) detected on Display0
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
OpenGL renderer: Apple M2 Max
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: Mac14,6
Model Number: MNWE3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 20 days, 22 hours, 15 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Crestron:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Mirror: On
Mirror Status: Hardware Mirror
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: 2022.2.22
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: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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