Opened 12 months ago

Closed 12 months ago

#16348 closed defect (nonchimerax)

Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics

Reported by: chimerax-bug-report@… 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",
  "coalitionID" : 7380,
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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,
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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 Eric Pettersen, 12 months ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Graphics hardware encountered an error and was reset

comment:2 by Tom Goddard, 12 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

Apple Intel graphics driver crash.

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