![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Closed 11 months ago
#16348 closed defect (nonchimerax)
Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.2.1-x86_64-i386-64bit
ChimeraX Version: 1.9rc202411190203 (2024-11-19 02:03:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff8582cf680 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX-1.9-rc2024.11.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1769 in set_multishadow_view
File "/Applications/ChimeraX-1.9-rc2024.11.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 251 in _draw_scene
File "/Applications/ChimeraX-1.9-rc2024.11.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.9-rc2024.11.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.9-rc2024.11.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.9-rc2024.11.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9-rc2024.11.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9-rc2024.11.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 55)
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{
"uptime" : 90000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir9,1",
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"build" : "22D68",
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"captureTime" : "2024-11-20 12:59:43.4492 -0800",
"incident" : "81C833FE-5BA3-4F15-8876-59D9F9A1BEBB",
"pid" : 16352,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-19 20:07:13.1101 -0800",
"procStartAbsTime" : 62563781375668,
"procExitAbsTime" : 90984452765610,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9-rc2024.11.19.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"B7B34B10-F41E-5016-ADDA-A635D4D2F993","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "52670452-3FA5-88B0-51D1-327A07C71996",
"throttleTimeout" : 2147483647,
"wakeTime" : 337,
"bridgeVersion" : {"build":"20P3045","train":"7.2"},
"sleepWakeUUID" : "2B9E166C-7C13-4A32-B88C-E7D6237D3EA8",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411190203 (2024-11-19)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> show atoms
> style stick
Changed 11946 atom styles
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> hide sel atoms
> select clear
> select add #1
11946 atoms, 12273 bonds, 81 pseudobonds, 1453 residues, 3 models selected
> select subtract #1
Nothing selected
> select clear
> name frozen "W-C base pair" sel
Not registering illegal selector name "W-C base pair"
> name frozen "W-C base pair" sel
Not registering illegal selector name "W-C base pair"
> name frozen "base pair" sel
Not registering illegal selector name "base pair"
> name frozen pair sel
> select pair
1 pseudobond, 1 model selected
No visible atoms, bonds, or surfaces selected
> select pair
1 pseudobond, 1 model selected
> select clear
> name frozen pair sel
> select pair
1 pseudobond, 1 model selected
> select pair
1 pseudobond, 1 model selected
> show atoms
> hide atoms
> show atoms
> select pair
1 pseudobond, 1 model selected
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> hide sel atoms
> select pair
1 pseudobond, 1 model selected
> color byhetero
> select clear
> close session
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> show atoms
> style stick
Changed 11946 atom styles
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> hide sel atoms
> name frozen pair sel
> sequence chain #1/A
Alignment identifier is 1/A
> hide target m
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 10653 atom styles
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> show atoms
> style stick
Changed 11946 atom styles
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> hide sel atoms
> name frozen pair sel
> select ~sel & ##selected
76 pseudobonds, 1 model selected
> hide atoms
> show atoms
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> show atoms
> style stick
Changed 11946 atom styles
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> hide sel atoms
> select clear
> name frozen pair sel
> select ~sel
11946 atoms, 12273 bonds, 81 pseudobonds, 1453 residues, 3 models selected
> hide (#!1 & sel) target a
> show target m
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> show atoms
> style stick
Changed 11946 atom styles
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> hide sel atoms
> select /J:28@OP2
1 atom, 1 residue, 1 model selected
> select /J:28@OP2
1 atom, 1 residue, 1 model selected
> select subtract /J:28@OP2
Nothing selected
> name frozen pair sel
> select ~sel & ##selected
76 pseudobonds, 1 model selected
> select ~sel
11946 atoms, 12273 bonds, 81 pseudobonds, 1453 residues, 3 models selected
> select clear
No visible atoms or bonds selected
> select pair
1 pseudobond, 1 model selected
> select ~sel & ##selected
Nothing selected
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> hide sel target a
> select /I
271 atoms, 304 bonds, 13 residues, 1 model selected
> select /H
387 atoms, 431 bonds, 19 residues, 1 model selected
> select /J
635 atoms, 713 bonds, 31 residues, 1 model selected
> select pair
1 pseudobond, 1 model selected
> show atoms
> hide atoms
> show atoms
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> hide sel atoms
> name frozen pair sel
> select pair
1 pseudobond, 1 model selected
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> show sel cartoons
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> hide atoms
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> show sel atoms
> show sel cartoons
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> hide cartoons
> hide atoms
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> show sel cartoons
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> select clear
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> set bgColor white
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select /B/C/D
5693 atoms, 5766 bonds, 5 pseudobonds, 750 residues, 2 models selected
> select clear
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select /B/C/D
5693 atoms, 5766 bonds, 5 pseudobonds, 750 residues, 2 models selected
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> show atoms
> style stick
Changed 11946 atom styles
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> hide sel atoms
> set bgColor black
> select clear
> name frozen pair sel
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> hide sel atoms
> select pair
1 pseudobond, 1 model selected
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> open P18858 fromDatabase uniprot associate #1/A
Summary of feedback from opening P18858 fetched from uniprot
---
notes | Fetching compressed P18858 UniProt info from https://www.uniprot.org/uniprot/P18858.xml
Alignment identifier is P18858
Associated 7qnz chain A to P18858 with 0 mismatches
Opened UniProt P18858
> select #1/A:1-919
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select #1/A:1-919
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> open P18858 fromDatabase uniprot associate #1/A
Summary of feedback from opening P18858 fetched from uniprot
---
notes | Destroying pre-existing alignment with identifier P18858
Alignment identifier is P18858
Associated 7qnz chain A to P18858 with 0 mismatches
Opened UniProt P18858
> select /A:568
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:568
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select clear
> hide atoms
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> show sel atoms
> hide sel atoms
> select ::name="AMP"
23 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> select ::name="AMP"
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select clear
> open 7QO1 fromDatabase pdb format mmcif
Summary of feedback from opening 7QO1 fetched from pdb
---
note | Fetching compressed mmCIF 7qo1 from http://files.rcsb.org/download/7qo1.cif
7qo1 title:
complex of DNA ligase I and FEN1 on PCNA and DNA [more info...]
Chain information for 7qo1 #2
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 161-919
B F G | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Y | Flap endonuclease 1 | FEN1_HUMAN 1-380
Non-standard residues in 7qo1 #2
---
AMP — adenosine monophosphate
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 7qnz, chain A (#1) with 7qo1, chain A (#2), sequence alignment
score = 3613.6
RMSD between 635 pruned atom pairs is 0.815 angstroms; (across all 640 pairs:
0.835)
> select protein
23539 atoms, 23923 bonds, 9 pseudobonds, 3084 residues, 4 models selected
> show sel cartoons
> select #1/A#2/A
9920 atoms, 10118 bonds, 1280 residues, 2 models selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 9920 atom styles
> close
> open 7QO1 format mmcif fromDatabase pdb
7qo1 title:
complex of DNA ligase I and FEN1 on PCNA and DNA [more info...]
Chain information for 7qo1 #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 161-919
B F G | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Y | Flap endonuclease 1 | FEN1_HUMAN 1-380
Non-standard residues in 7qo1 #1
---
AMP — adenosine monophosphate
> open 7QO1 fromDatabase pdb format mmcif
7qo1 title:
complex of DNA ligase I and FEN1 on PCNA and DNA [more info...]
Chain information for 7qo1 #2
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 161-919
B F G | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Y | Flap endonuclease 1 | FEN1_HUMAN 1-380
Non-standard residues in 7qo1 #2
---
AMP — adenosine monophosphate
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> open 7QO1 fromDatabase pdb format mmcif
7qo1 title:
complex of DNA ligase I and FEN1 on PCNA and DNA [more info...]
Chain information for 7qo1 #2
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 161-919
B F G | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Y | Flap endonuclease 1 | FEN1_HUMAN 1-380
Non-standard residues in 7qo1 #2
---
AMP — adenosine monophosphate
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 7qnz, chain A (#1) with 7qo1, chain A (#2), sequence alignment
score = 3613.6
RMSD between 635 pruned atom pairs is 0.815 angstroms; (across all 640 pairs:
0.835)
> select protein
23539 atoms, 23923 bonds, 9 pseudobonds, 3084 residues, 4 models selected
> show sel cartoons
> select #1/A#2/A
9920 atoms, 10118 bonds, 1280 residues, 2 models selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 9920 atom styles
> select #1/A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> hide sel atoms
> show sel atoms
> select #1/A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> hide target m
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> open 7QO1 fromDatabase pdb format mmcif
7qo1 title:
complex of DNA ligase I and FEN1 on PCNA and DNA [more info...]
Chain information for 7qo1 #2
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 161-919
B F G | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Y | Flap endonuclease 1 | FEN1_HUMAN 1-380
Non-standard residues in 7qo1 #2
---
AMP — adenosine monophosphate
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 7qnz, chain A (#1) with 7qo1, chain A (#2), sequence alignment
score = 3613.6
RMSD between 635 pruned atom pairs is 0.815 angstroms; (across all 640 pairs:
0.835)
> select protein
23539 atoms, 23923 bonds, 9 pseudobonds, 3084 residues, 4 models selected
> show sel cartoons
> select #1/A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 4960 atom styles
> select #2/A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 4960 atom styles
> select #1/A#2/A
9920 atoms, 10118 bonds, 1280 residues, 2 models selected
> color sel red
> select #1/A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> color sel light sea green
> select #2/A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> color sel orange
> select #1/A:669
6 atoms, 5 bonds, 1 residue, 1 model selected
> select protein
23539 atoms, 23923 bonds, 9 pseudobonds, 3084 residues, 4 models selected
> hide sel atoms
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> show atoms
> style stick
Changed 11946 atom styles
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> hide sel atoms
> select clear
> name frozen pair sel
> select pair
1 pseudobond, 1 model selected
> select add /J:27@N7
1 atom, 8 bonds, 3 pseudobonds, 1 residue, 2 models selected
> select add /J:27@C1'
2 atoms, 12 bonds, 3 pseudobonds, 1 residue, 2 models selected
> select add /J:28@OP1
3 atoms, 19 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select subtract /J:28@OP1
2 atoms, 19 bonds, 3 pseudobonds, 1 residue, 2 models selected
> select add /J:28@OP1
3 atoms, 19 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select add /J:28@OP2
4 atoms, 21 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select add /H:5@N3
5 atoms, 22 bonds, 3 pseudobonds, 3 residues, 2 models selected
> select add /H:5@N4
6 atoms, 24 bonds, 3 pseudobonds, 3 residues, 2 models selected
> select add /H:5@N1
7 atoms, 27 bonds, 3 pseudobonds, 3 residues, 2 models selected
> select add /H:6@OP1
8 atoms, 38 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select add /H:6@OP2
9 atoms, 38 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select subtract /H:6@OP2
8 atoms, 38 bonds, 3 pseudobonds, 4 residues, 2 models selected
> name frozen pair sel
> select /J
635 atoms, 713 bonds, 31 residues, 1 model selected
> hide sel atoms
> select /H
387 atoms, 431 bonds, 19 residues, 1 model selected
> hide sel atoms
> select pair
8 atoms, 39 bonds, 3 pseudobonds, 4 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> show atoms
> style stick
Changed 11946 atom styles
> style stick
Changed 11946 atom styles
> select protein
10653 atoms, 10825 bonds, 5 pseudobonds, 1390 residues, 2 models selected
> hide sel atoms
> select /h 2
Expected a keyword
> select /h:2
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add /H:2@N3
1 atom, 2 pseudobonds, 1 residue, 2 models selected
> select add /H:2@N1
2 atoms, 7 bonds, 2 pseudobonds, 1 residue, 2 models selected
> select add /H:2@O2
3 atoms, 8 bonds, 2 pseudobonds, 1 residue, 2 models selected
> select add /J:30@C6
4 atoms, 9 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select add /J:30@N1
5 atoms, 9 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select subtract /J:30@C6
4 atoms, 8 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select add /J:30@O6
5 atoms, 10 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select add /J:30@C2
6 atoms, 11 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select add /J:30@N2
7 atoms, 11 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select add /H:2@O4'
8 atoms, 16 bonds, 3 pseudobonds, 2 residues, 2 models selected
Drag select of 4 atoms, 1 pseudobonds, 4 bonds
Drag select of 10 atoms, 3 pseudobonds, 8 bonds
> select clear
Drag select of 3 atoms, 1 pseudobonds, 3 bonds
> select add /H:2@O2
4 atoms, 4 bonds, 1 pseudobond, 1 residue, 2 models selected
Drag select of 2 bonds
Drag select of 2 atoms, 3 bonds
> select add /H:2@C5'
7 atoms, 15 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add /H:2@O5'
8 atoms, 15 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add /H:2@OP1
9 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add /H:2@OP2
10 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add /H:3@OP2
11 atoms, 22 bonds, 1 pseudobond, 2 residues, 2 models selected
> select add /H:1@O3'
12 atoms, 24 bonds, 1 pseudobond, 3 residues, 2 models selected
> select add /H:1@OP1
13 atoms, 29 bonds, 1 pseudobond, 3 residues, 2 models selected
> select add /J:30@C2
14 atoms, 24 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select add /J:30@N2
15 atoms, 25 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select add /J:30@C4
16 atoms, 30 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select add /J:30@N3
17 atoms, 31 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select add /J:30@C1'
18 atoms, 37 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select add /J:31@OP2
19 atoms, 39 bonds, 3 pseudobonds, 5 residues, 2 models selected
> select add /J:31@OP1
20 atoms, 41 bonds, 3 pseudobonds, 5 residues, 2 models selected
> select add /J:30@C3'
21 atoms, 45 bonds, 3 pseudobonds, 5 residues, 2 models selected
> select add /J:30@C4'
22 atoms, 45 bonds, 3 pseudobonds, 5 residues, 2 models selected
> select subtract /J:30@C4'
21 atoms, 43 bonds, 3 pseudobonds, 5 residues, 2 models selected
> select add /J:30@C2'
22 atoms, 46 bonds, 3 pseudobonds, 5 residues, 2 models selected
> select add /J:30@O4'
23 atoms, 46 bonds, 3 pseudobonds, 5 residues, 2 models selected
> select add /J:30@N7
24 atoms, 46 bonds, 3 pseudobonds, 5 residues, 2 models selected
> select add /J:30@C8
25 atoms, 46 bonds, 3 pseudobonds, 5 residues, 2 models selected
> select add /J:30@O6
26 atoms, 46 bonds, 3 pseudobonds, 5 residues, 2 models selected
> name frozen pair sel
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select /J
635 atoms, 713 bonds, 31 residues, 1 model selected
> hide sel atoms
> select /H
387 atoms, 431 bonds, 19 residues, 1 model selected
> hide sel atoms
> select pair
26 atoms, 46 bonds, 3 pseudobonds, 5 residues, 2 models selected
> show sel atoms
> select clear
> select /H
387 atoms, 431 bonds, 19 residues, 1 model selected
> show sel atoms
> select /J
635 atoms, 713 bonds, 31 residues, 1 model selected
> show sel atoms
> select /h:2
19 atoms, 20 bonds, 1 residue, 1 model selected
> name frozen "C base" sel
Not registering illegal selector name "C base"
> select /j:30
22 atoms, 24 bonds, 1 residue, 1 model selected
> select pair
26 atoms, 46 bonds, 3 pseudobonds, 5 residues, 2 models selected
> select /j:30
22 atoms, 24 bonds, 1 residue, 1 model selected
> name frozen "C base" sel
Not registering illegal selector name "C base"
> name frozen "C base" sel
Not registering illegal selector name "C base"
> name frozen "C base" sel
Not registering illegal selector name "C base"
> name frozen "C base" sel
Not registering illegal selector name "C base"
> select clear
> select /j:30
22 atoms, 24 bonds, 1 residue, 1 model selected
> name frozen C sel
"C" is reserved and cannot be redefined
> name frozen Cbase sel
> select /h:2
19 atoms, 20 bonds, 1 residue, 1 model selected
> name frozen Gbase sel
> select /H
387 atoms, 431 bonds, 19 residues, 1 model selected
> hide sel atoms
> select /H
387 atoms, 431 bonds, 19 residues, 1 model selected
> select /J
635 atoms, 713 bonds, 31 residues, 1 model selected
> hide sel atoms
> select Cbase
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select Gbase
19 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 39 atoms, 3 pseudobonds, 44 bonds
Drag select of 41 atoms, 3 pseudobonds, 44 bonds
> select
11946 atoms, 12273 bonds, 81 pseudobonds, 1453 residues, 3 models selected
> name frozen GCpair sel
> set bgColor white
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> set bgColor black
> select /I
271 atoms, 304 bonds, 13 residues, 1 model selected
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select clear
> select
11946 atoms, 12273 bonds, 81 pseudobonds, 1453 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 11946 atom styles
> select /H
387 atoms, 431 bonds, 19 residues, 1 model selected
> hide sel atoms
> select /H
387 atoms, 431 bonds, 19 residues, 1 model selected
> hide sel atoms
> select /H
387 atoms, 431 bonds, 19 residues, 1 model selected
> hide sel atoms
> select /B/C/D
5693 atoms, 5766 bonds, 5 pseudobonds, 750 residues, 2 models selected
> hide sel atoms
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> hide sel atoms
> select /a:568,621,573,589
40 atoms, 36 bonds, 4 residues, 1 model selected
> select /a:568,621,573,589
40 atoms, 36 bonds, 4 residues, 1 model selected
> select /a:568,621,573,589
40 atoms, 36 bonds, 4 residues, 1 model selected
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select /A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> show sel atoms
> select /a:568,621,573,589
40 atoms, 36 bonds, 4 residues, 1 model selected
> name frozen ACresidues sel
> select
11946 atoms, 12273 bonds, 81 pseudobonds, 1453 residues, 3 models selected
> hide sel atoms
> select ACresidues
40 atoms, 36 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select /I
271 atoms, 304 bonds, 13 residues, 1 model selected
> show sel atoms
> ui tool show Distances
> select /A:573@N
1 atom, 1 residue, 1 model selected
> select add /A:621@OE1
2 atoms, 2 residues, 1 model selected
> distance /A:573@N /A:621@OE1
Distance between /A ARG 573 N and GLU 621 OE1: 3.223Å
> select /A:573@O
1 atom, 1 residue, 1 model selected
> select /A:589@N
1 atom, 1 residue, 1 model selected
> select add /A:573@O
2 atoms, 2 residues, 1 model selected
> distance /A:589@N /A:573@O
Distance between /A ARG 589 N and ARG 573 O: 4.476Å
> ~distance /A:573@N /A:621@OE1
> ~distance /A:589@N /A:573@O
> select /A:573@N
1 atom, 1 residue, 1 model selected
> select add /A:621@OE1
2 atoms, 2 residues, 1 model selected
> distance /A:573@N /A:621@OE1
Distance between /A ARG 573 N and GLU 621 OE1: 3.223Å
> select /A:573@O
1 atom, 1 residue, 1 model selected
> select add /A:621@N
2 atoms, 2 residues, 1 model selected
> distance /A:573@O /A:621@N
Distance between /A ARG 573 O and GLU 621 N: 6.345Å
> ~distance /A:573@O /A:621@N
> select clear
> select /I:100@O1P
1 atom, 1 residue, 1 model selected
> select add /A:568@NZ
2 atoms, 2 residues, 1 model selected
> distance /I:100@O1P /A:568@NZ
Distance between /I AMP 100 O1P and /A LYS 568 NZ: 2.867Å
> select /I:100@O3'
1 atom, 1 residue, 1 model selected
> select add /A:573@NH2
2 atoms, 2 residues, 1 model selected
> distance /I:100@O3' /A:573@NH2
Distance between /I AMP 100 O3' and /A ARG 573 NH2: 2.617Å
> select /I:100@O2'
1 atom, 1 residue, 1 model selected
> select add /A:573@NH1
2 atoms, 2 residues, 1 model selected
> distance /I:100@O2' /A:573@NH1
Distance between /I AMP 100 O2' and /A ARG 573 NH1: 5.935Å
> ~distance /I:100@O2' /A:573@NH1
> select /I:100@O2'
1 atom, 1 residue, 1 model selected
> select /I:100@O2'
1 atom, 1 residue, 1 model selected
> select /I:100@O2'
1 atom, 1 residue, 1 model selected
> select subtract /I:100@O2'
Nothing selected
> select /A:573@O
1 atom, 1 residue, 1 model selected
> select add /A:621@N
2 atoms, 2 residues, 1 model selected
> distance /A:573@O /A:621@N
Distance between /A ARG 573 O and GLU 621 N: 6.345Å
> select /I:100@N6
1 atom, 1 residue, 1 model selected
> select /A:568@O
1 atom, 1 residue, 1 model selected
> select add /I:100@N6
2 atoms, 2 residues, 1 model selected
> distance /A:568@O /I:100@N6
Distance between /A LYS 568 O and /I AMP 100 N6: 7.205Å
> select /A:573@N
1 atom, 1 residue, 1 model selected
> select add /I:100@O2'
2 atoms, 2 residues, 1 model selected
> distance /A:573@N /I:100@O2'
Distance between /A ARG 573 N and /I AMP 100 O2': 3.393Å
> ~distance /A:573@N /A:621@OE1
> ~distance /A:573@O /A:621@N
> ~distance /A:568@O /I:100@N6
> select clear
> select /I:100@O4'
1 atom, 1 residue, 1 model selected
> select add /A:568@NZ
2 atoms, 2 residues, 1 model selected
> distance /I:100@O4' /A:568@NZ
Distance between /I AMP 100 O4' and /A LYS 568 NZ: 2.922Å
> set bgColor white
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> set bgColor black
> open 7QO1 fromDatabase pdb format mmcif
7qo1 title:
complex of DNA ligase I and FEN1 on PCNA and DNA [more info...]
Chain information for 7qo1 #2
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 161-919
B F G | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Y | Flap endonuclease 1 | FEN1_HUMAN 1-380
Non-standard residues in 7qo1 #2
---
AMP — adenosine monophosphate
> close
> open 7QNZ format mmcif fromDatabase pdb
7qnz title:
human Lig1-DNA-PCNA complex reconstituted in absence of ATP [more info...]
Chain information for 7qnz #1
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 1-919
B C D | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Non-standard residues in 7qnz #1
---
AMP — adenosine monophosphate
> open 7QO1 fromDatabase pdb format mmcif
7qo1 title:
complex of DNA ligase I and FEN1 on PCNA and DNA [more info...]
Chain information for 7qo1 #2
---
Chain | Description | UniProt
A | DNA ligase 1 | DNLI1_HUMAN 161-919
B F G | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261
H | Oligo19ddC |
I | Oligo13P |
J | Oligo32 |
Y | Flap endonuclease 1 | FEN1_HUMAN 1-380
Non-standard residues in 7qo1 #2
---
AMP — adenosine monophosphate
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
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 7qnz, chain A (#1) with 7qo1, chain A (#2), sequence alignment
score = 3613.6
RMSD between 635 pruned atom pairs is 0.815 angstroms; (across all 640 pairs:
0.835)
> select protein
23539 atoms, 23923 bonds, 9 pseudobonds, 3084 residues, 4 models selected
> show sel cartoons
> select #1/A#2/A
9920 atoms, 10118 bonds, 1280 residues, 2 models selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 9920 atom styles
> show sel cartoons
> hide sel atoms
> select
26125 atoms, 26819 bonds, 161 pseudobonds, 3210 residues, 6 models selected
> show sel cartoons
> select protein
23539 atoms, 23923 bonds, 9 pseudobonds, 3084 residues, 4 models selected
> select #1/A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select #1/I#2/I
542 atoms, 608 bonds, 26 residues, 2 models selected
> select #1/H#2/H
774 atoms, 862 bonds, 38 residues, 2 models selected
> show sel cartoons
> select #1/I#2/I
542 atoms, 608 bonds, 26 residues, 2 models selected
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> hide sel surfaces
> select #1/I#2/I
542 atoms, 608 bonds, 26 residues, 2 models selected
> select #1/H#2/H
774 atoms, 862 bonds, 38 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #1/J#2/J
1270 atoms, 1426 bonds, 62 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #1/B#1/C#1/D#2/B#2/F#2/G
11421 atoms, 11570 bonds, 7 pseudobonds, 1503 residues, 4 models selected
> hide sel atoms
> select #1/B#1/C#1/D#2/B#2/F#2/G
11421 atoms, 11570 bonds, 7 pseudobonds, 1503 residues, 4 models selected
> select #2/Y
2198 atoms, 2235 bonds, 2 pseudobonds, 301 residues, 2 models selected
> hide sel atoms
> select #1/A#2/A
9920 atoms, 10118 bonds, 1280 residues, 2 models selected
> style sel stick
Changed 9920 atom styles
> select #1/I#2/I
542 atoms, 608 bonds, 26 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 542 atom styles
> select #1/H#2/H
774 atoms, 862 bonds, 38 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 774 atom styles
> select #1/J#2/J
1270 atoms, 1426 bonds, 62 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 1270 atom styles
> select #1/A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> color sel hot pink
> select #2/A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> color sel blue
> select #1/I
271 atoms, 304 bonds, 13 residues, 1 model selected
> color sel cyan
> select #2/I
271 atoms, 304 bonds, 13 residues, 1 model selected
> color sel magenta
> color sel yellow
> select #1/H
387 atoms, 431 bonds, 19 residues, 1 model selected
> color sel red
> select #2/H
387 atoms, 431 bonds, 19 residues, 1 model selected
> color sel light sea green
> select #1/J
635 atoms, 713 bonds, 31 residues, 1 model selected
> color sel red
> color sel forest green
> color sel lime
> select #2/J
635 atoms, 713 bonds, 31 residues, 1 model selected
> color sel light gray
> select #1/A
4960 atoms, 5059 bonds, 640 residues, 1 model selected
> select #1/B#1/C#1/D#2/B#2/F#2/G
11421 atoms, 11570 bonds, 7 pseudobonds, 1503 residues, 4 models selected
> ui mousemode right rotate
> ui mousemode right zoom
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> save /Users/khloevu/Desktop/image1.png supersample 3
> save /Users/khloevu/Desktop/image2.png supersample 3
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411190203 (2024-11-19)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir9,1
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.1 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
OS Loader Version: 564.40.4~66
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 8 days, 15 hours, 38 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a51
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9rc202411190203
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.11
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.3.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.8
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 11 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics |
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Apple Intel graphics driver crash.