![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Last modified 16 months ago
#15657 assigned defect
Qt fatal error: Failed to initialize graphics backend for OpenGL
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.3.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Qt fatal error: Failed to initialize graphics backend for OpenGL.
Fatal Python error: Aborted
Current thread 0x0000000202915240 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 861 in rapid_access_shown
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 198 in build
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 722 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util (total: 45)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
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"captureTime" : "2024-07-24 08:49:30.7299 +0900",
"codeSigningMonitor" : 1,
"incident" : "608E4A82-2219-4B45-B7EC-3AC6B51EC74E",
"pid" : 21703,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-24 08:49:28.2132 +0900",
"procStartAbsTime" : 33412438070221,
"procExitAbsTime" : 33412498390583,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "286E4181-0333-903E-6993-0E6928266046",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 3115,
"sleepWakeUUID" : "950F7167-9679-4728-9024-0CE8A139C9EF",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":21703},
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"faultingThread" : 0,
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Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/AtCENH3-nuc_Tal1_EVADE.cxs
Log from Tue Jul 2 13:03:40 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_hsch3_nuc_601/fold_cc_hsch3_nuc_601_model_0.cif
Chain information for fold_cc_hsch3_nuc_601_model_0.cif #1
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
K | .
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_hsch3_nuc_601/fold_cc_hsch3_nuc_601_model_1.cif
Chain information for fold_cc_hsch3_nuc_601_model_1.cif #2
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
K | .
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_hsch3_nuc_601/fold_cc_hsch3_nuc_601_model_2.cif
Chain information for fold_cc_hsch3_nuc_601_model_2.cif #3
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
K | .
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_hsch3_nuc_601/fold_cc_hsch3_nuc_601_model_3.cif
Chain information for fold_cc_hsch3_nuc_601_model_3.cif #4
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
K | .
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_hsch3_nuc_601/fold_cc_hsch3_nuc_601_model_4.cif
Chain information for fold_cc_hsch3_nuc_601_model_4.cif #5
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
K | .
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/K
Alignment identifier is 1/K
> ui tool show "Show Sequence Viewer"
> sequence chain #1/K
Alignment identifier is 1/K
> ui tool show "Show Sequence Viewer"
> sequence chain #1/J
Alignment identifier is 1/J
> ui tool show "Show Sequence Viewer"
> sequence chain #1/I
Alignment identifier is 1/I
> select #1/I:426
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/I:426-537
908 atoms, 921 bonds, 112 residues, 1 model selected
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_short_ch3_nuc_601/fold_cc_short_ch3_nuc_601_model_0.cif
Chain information for fold_cc_short_ch3_nuc_601_model_0.cif #6
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
K | .
> ui tool show "Show Sequence Viewer"
> sequence chain #6/I
Alignment identifier is 6/I
> hide #1 models
> select #6/I:62-112
427 atoms, 433 bonds, 51 residues, 1 model selected
> select #6/I:57-112
461 atoms, 467 bonds, 56 residues, 1 model selected
> hide #6 models
> show #1 models
> select #1/I:537-538
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/I:517-538
189 atoms, 193 bonds, 22 residues, 1 model selected
> select #1/I
7502 atoms, 7630 bonds, 943 residues, 1 model selected
> 1-425
Unknown command: 1-425
> select #1/I
7502 atoms, 7630 bonds, 943 residues, 1 model selected
> 1:425
Unknown command: 1:425
> select #1/I
7502 atoms, 7630 bonds, 943 residues, 1 model selected
> 1 425
Unknown command: 1 425
> select #1/I
7502 atoms, 7630 bonds, 943 residues, 1 model selected
> 425
Unknown command: 425
> select #1/I: 425
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/I: 1-425
3372 atoms, 3429 bonds, 425 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1/I: 538--943
Nothing selected
> select #1/I: 538-943
3222 atoms, 3278 bonds, 406 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #1/I:517-538
189 atoms, 193 bonds, 22 residues, 1 model selected
> select #1/I:538
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/I:522-538
149 atoms, 153 bonds, 17 residues, 1 model selected
> select #1/E,F
2244 atoms, 2296 bonds, 278 residues, 1 model selected
> show #6 models
> ui tool show Matchmaker
> matchmaker #6/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_cc_short_ch3_nuc_601_model_0.cif, chain E (#6), sequence alignment score
= 601.8
RMSD between 97 pruned atom pairs is 0.254 angstroms; (across all 139 pairs:
15.946)
> ui tool show Matchmaker
> matchmaker #6/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_cc_short_ch3_nuc_601_model_0.cif, chain F (#6), sequence alignment score
= 601.8
RMSD between 97 pruned atom pairs is 0.258 angstroms; (across all 139 pairs:
16.298)
> matchmaker #6/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_cc_short_ch3_nuc_601_model_0.cif, chain F (#6), sequence alignment score
= 601.8
RMSD between 97 pruned atom pairs is 0.258 angstroms; (across all 139 pairs:
16.298)
> select clear
> select #1/I
7502 atoms, 7630 bonds, 943 residues, 1 model selected
> color sel red
> select #1/A-H
7742 atoms, 7864 bonds, 990 residues, 1 model selected
> color sel light gray
> select #1/E,F
2244 atoms, 2296 bonds, 278 residues, 1 model selected
> color sel light sea green
> select #1/J,K
6931 atoms, 7774 bonds, 338 residues, 1 model selected
> color sel light gray
> select #6/J,K
6931 atoms, 7774 bonds, 338 residues, 1 model selected
> color sel light gray
> select #6/A-H
7742 atoms, 7864 bonds, 990 residues, 1 model selected
> color sel light gray
> select #6/E,F
2244 atoms, 2296 bonds, 278 residues, 1 model selected
> color sel lime
> select #6/I
909 atoms, 922 bonds, 112 residues, 1 model selected
> color sel orange
> hide #6 models
> show #6 models
> select add #1
23084 atoms, 24190 bonds, 2383 residues, 2 models selected
> select add #6
37757 atoms, 39828 bonds, 3711 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> select #1/I: 1-425
3372 atoms, 3429 bonds, 425 residues, 1 model selected
> hide sel cartoons
> select #1/I: 538-943
3222 atoms, 3278 bonds, 406 residues, 1 model selected
> hide sel cartoons
> save
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/HsCENH3-nuc_CCfull_CC426-537.cxs
> open /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/6mup.pdb
6mup.pdb title:
Cenp-A nucleosome bound by two copies of cenp-C(Cd) and two copies cenp-N(NT)
[more info...]
Chain information for 6mup.pdb #7
---
Chain | Description | UniProt
A E | histone H3-like centromeric protein A | CENPA_HUMAN 38-139
B F | histone H4 | H4_HUMAN 8-101
C G | histone H2A/L | H2A1C_HUMAN 13-117
D H | histone H2B type 2-F | H2B2F_HUMAN 33-124
I | DNA (147-mer) |
J | DNA (147-mer) |
K L | centromere protein C | CENPC_HUMAN 518-537
M N | centromere protein N | CENPN_HUMAN 1-212
> open /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/6se6.pdb
6se6.pdb title:
CLASS2 : cenp-A nucleosome In complex with cenp-C central region [more
info...]
Chain information for 6se6.pdb #8
---
Chain | Description | UniProt
A E | histone H3-like centromeric protein A | CENPA_HUMAN 1-140
B F | histone H4 | H4_HUMAN 0-102
C G | histone H2A type 2-A | H2A2A_HUMAN 0-129
D H | histone H2B type 1-C/E/F/G/I | H2B1C_HUMAN 0-125
I | DNA (145-mer) |
J | DNA (145-mer) |
V | centromere protein C | CENPC_HUMAN 426-537
> select #7/A,E
1623 atoms, 1653 bonds, 203 residues, 1 model selected
> select add #7
15803 atoms, 16702 bonds, 2 pseudobonds, 1518 residues, 2 models selected
> select add #8
27871 atoms, 29582 bonds, 2 pseudobonds, 2579 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> color (#8#!7 & sel) light gray
> select #7/A,E
1623 atoms, 1653 bonds, 203 residues, 1 model selected
> color sel forest green
> select #8/A,E
1624 atoms, 1654 bonds, 196 residues, 1 model selected
> color sel forest green
> ui tool show Matchmaker
> matchmaker #7/A to #6/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_short_ch3_nuc_601_model_0.cif, chain E (#6) with 6mup.pdb,
chain A (#7), sequence alignment score = 440.4
RMSD between 90 pruned atom pairs is 0.526 angstroms; (across all 102 pairs:
1.235)
> matchmaker #7/A to #6/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_short_ch3_nuc_601_model_0.cif, chain E (#6) with 6mup.pdb,
chain A (#7), sequence alignment score = 440.4
RMSD between 90 pruned atom pairs is 0.526 angstroms; (across all 102 pairs:
1.235)
> select #7/K,L
343 atoms, 351 bonds, 39 residues, 1 model selected
> color sel magenta
> select clear
> hide #8 models
> save
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/HsCENH3-nuc_CCfull_CC426-537.cxs
> hide #2-5 target m
> close #2-5
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601/fold_ch3_nuc_601_model_0.cif
Chain information for fold_ch3_nuc_601_model_0.cif #2
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
> ui tool show Matchmaker
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_hsch3_nuc_601/fold_hsch3_nuc_601_model_0.cif
Chain information for fold_hsch3_nuc_601_model_0.cif #3
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
> hide #6 models
> hide #!7 models
> hide #1 models
> select #2,3
30170 atoms, 32104 bonds, 2784 residues, 2 models selected
> color sel light gray
> hide sel atoms
> show sel cartoons
> select #2,3/E,F
4996 atoms, 5098 bonds, 632 residues, 2 models selected
> color sel cyan
> show #1 models
> ui tool show Matchmaker
> matchmaker #2/E to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_model_0.cif, chain E (#2), sequence alignment score = 96.8
RMSD between 50 pruned atom pairs is 0.967 angstroms; (across all 89 pairs:
14.355)
> matchmaker #3/E to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 118.7
RMSD between 50 pruned atom pairs is 1.037 angstroms; (across all 90 pairs:
13.968)
> matchmaker #3/E to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 118.7
RMSD between 50 pruned atom pairs is 1.037 angstroms; (across all 90 pairs:
13.968)
> select add #3
17425 atoms, 18440 bonds, 1682 residues, 2 models selected
> select add #2
30170 atoms, 32104 bonds, 2784 residues, 2 models selected
> select subtract #3
15497 atoms, 16466 bonds, 1456 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #2 models
> hide #3 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> ui tool show Matchmaker
> matchmaker #2/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_model_0.cif, chain E (#2), sequence alignment score = 233.6
RMSD between 86 pruned atom pairs is 0.451 angstroms; (across all 114 pairs:
17.583)
> matchmaker #2/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_model_0.cif, chain F (#2), sequence alignment score = 233.6
RMSD between 86 pruned atom pairs is 0.453 angstroms; (across all 114 pairs:
16.825)
> matchmaker #2/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_model_0.cif, chain F (#2), sequence alignment score = 233.6
RMSD between 86 pruned atom pairs is 0.453 angstroms; (across all 114 pairs:
16.825)
> show #3 models
> hide #1 models
> ui tool show Matchmaker
> matchmaker #3/F to #2/F pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ch3_nuc_601_model_0.cif, chain F (#2) with
fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 320.9
RMSD between 80 pruned atom pairs is 0.461 angstroms; (across all 134 pairs:
35.917)
> matchmaker #3/F to #2/F pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ch3_nuc_601_model_0.cif, chain F (#2) with
fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 320.9
RMSD between 80 pruned atom pairs is 0.461 angstroms; (across all 134 pairs:
35.917)
> hide #2 models
> show #1 models
> save
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/AtvsHsCENH3-nuc_CCfull_CC426-537.cxs
> hide #3 models
> show #3 models
> hide #1 models
> show #1 models
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_atcc_full/fold_ch3_nuc_601_atcc_full_model_0.cif
Chain information for fold_ch3_nuc_601_atcc_full_model_0.cif #4
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
K | .
> select #4
21050 atoms, 22126 bonds, 2161 residues, 1 model selected
> color sel light gray
> select #4/E,f
2752 atoms, 2802 bonds, 354 residues, 1 model selected
> select #4/E,F
2752 atoms, 2802 bonds, 354 residues, 1 model selected
> color sel cyan
> select #4
21050 atoms, 22126 bonds, 2161 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #4/K
3484 atoms, 3911 bonds, 169 residues, 1 model selected
> select #4/I
5553 atoms, 5660 bonds, 705 residues, 1 model selected
> color sel yellow
> ui tool show Matchmaker
> matchmaker #4/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain F (#4), sequence alignment score
= 308
RMSD between 85 pruned atom pairs is 0.426 angstroms; (across all 135 pairs:
15.366)
> matchmaker #4/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score
= 308
RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs:
14.027)
> matchmaker #4/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score
= 308
RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs:
14.027)
> ui tool show Matchmaker
> matchmaker #4/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score
= 308
RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs:
14.027)
> matchmaker #3/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 604.8
RMSD between 8 pruned atom pairs is 1.210 angstroms; (across all 139 pairs:
24.773)
> matchmaker #3/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8
RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs:
24.430)
> matchmaker #3/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8
RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs:
24.430)
> hide #4 models
> select add #4
21050 atoms, 22126 bonds, 2161 residues, 1 model selected
> select subtract #4
Nothing selected
> ui tool show Matchmaker
> matchmaker #3/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8
RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs:
24.430)
> matchmaker #3/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 604.8
RMSD between 8 pruned atom pairs is 1.210 angstroms; (across all 139 pairs:
24.773)
> select #1/E
1122 atoms, 1148 bonds, 139 residues, 1 model selected
> select #3/E
1122 atoms, 1148 bonds, 139 residues, 1 model selected
> hide #3 models
> show #3 models
> hide #1 models
> show #1 models
> ui tool show Matchmaker
> matchmaker #3/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8
RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs:
24.430)
> matchmaker #3/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8
RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs:
24.430)
> ui tool show Matchmaker
> matchmaker #3/E to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 118.7
RMSD between 50 pruned atom pairs is 1.037 angstroms; (across all 90 pairs:
13.968)
> ui tool show Matchmaker
> matchmaker #3/F to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 118.7
RMSD between 49 pruned atom pairs is 1.012 angstroms; (across all 90 pairs:
13.942)
> matchmaker #3/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8
RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs:
24.430)
> matchmaker #3/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 604.8
RMSD between 8 pruned atom pairs is 1.210 angstroms; (across all 139 pairs:
24.773)
> matchmaker #3/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_hsch3_nuc_601_model_0.cif, chain A (#3), sequence alignment score = 578.1
RMSD between 106 pruned atom pairs is 0.202 angstroms; (across all 129 pairs:
4.154)
> matchmaker #3/B to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_hsch3_nuc_601_model_0.cif, chain B (#3), sequence alignment score = 578.1
RMSD between 106 pruned atom pairs is 0.202 angstroms; (across all 129 pairs:
4.327)
> matchmaker #3/B to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_hsch3_nuc_601_model_0.cif, chain B (#3), sequence alignment score = 578.1
RMSD between 106 pruned atom pairs is 0.202 angstroms; (across all 129 pairs:
4.327)
> select add #3
14673 atoms, 15638 bonds, 1328 residues, 1 model selected
> select subtract #3
Nothing selected
> show #4 models
> hide #3 models
> hide #1 models
> show #3 models
> hide #3 models
> show #1 models
> ui tool show Matchmaker
> matchmaker #4/E to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score
= 103.6
RMSD between 48 pruned atom pairs is 0.938 angstroms; (across all 96 pairs:
18.224)
> matchmaker #4/E to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score
= 103.6
RMSD between 48 pruned atom pairs is 0.938 angstroms; (across all 96 pairs:
18.224)
> ui tool show Matchmaker
> matchmaker #4/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain F (#4), sequence alignment score
= 308
RMSD between 85 pruned atom pairs is 0.426 angstroms; (across all 135 pairs:
15.366)
> ui tool show Matchmaker
> matchmaker #4/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score
= 308
RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs:
14.027)
> matchmaker #4/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score
= 308
RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs:
14.027)
> ui tool show Matchmaker
> matchmaker #4/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score
= 308
RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs:
14.027)
> matchmaker #4/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain F (#4), sequence alignment score
= 308
RMSD between 85 pruned atom pairs is 0.426 angstroms; (across all 135 pairs:
15.366)
> matchmaker #4/F to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with
fold_ch3_nuc_601_atcc_full_model_0.cif, chain F (#4), sequence alignment score
= 308
RMSD between 85 pruned atom pairs is 0.426 angstroms; (across all 135 pairs:
15.366)
> save
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/AtvsHsCENH3-nuc_CCfull_CC426-537.cxs
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_tal1_dimer/fold_tal1_dimer_model_0.cif
Chain information for fold_tal1_dimer_model_0.cif #5
---
Chain | Description
A B | .
> close #5
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_tal1_integrase_long_dimer/fold_tal1_integrase_long_dimer_model_0.cif
Chain information for fold_tal1_integrase_long_dimer_model_0.cif #5
---
Chain | Description
A | .
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_evade_integrase_long_dimer/fold_evade_integrase_long_dimer_model_0.cif
Chain information for fold_evade_integrase_long_dimer_model_0.cif #9
---
Chain | Description
A | .
> hide #1 models
> hide #4 models
> ui tool show Matchmaker
> matchmaker #9/A to #5/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_tal1_integrase_long_dimer_model_0.cif, chain A (#5) with
fold_evade_integrase_long_dimer_model_0.cif, chain A (#9), sequence alignment
score = 2141.7
RMSD between 249 pruned atom pairs is 0.422 angstroms; (across all 510 pairs:
28.859)
> matchmaker #9/A to #5/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_tal1_integrase_long_dimer_model_0.cif, chain A (#5) with
fold_evade_integrase_long_dimer_model_0.cif, chain A (#9), sequence alignment
score = 2141.7
RMSD between 249 pruned atom pairs is 0.422 angstroms; (across all 510 pairs:
28.859)
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:55-56
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/A:55-108
419 atoms, 432 bonds, 54 residues, 1 model selected
> select #5/A:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:56-310
2057 atoms, 2111 bonds, 255 residues, 1 model selected
> select #5/A:6-56
381 atoms, 389 bonds, 51 residues, 1 model selected
> select #5/A:6-107
778 atoms, 799 bonds, 102 residues, 1 model selected
> select #5/A:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:56-496
3542 atoms, 3633 bonds, 441 residues, 1 model selected
> select #5/A:481
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/A:481-490
88 atoms, 92 bonds, 10 residues, 1 model selected
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer/fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif
Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif #10
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K | .
L | .
> select add #10
24217 atoms, 25406 bonds, 2550 residues, 2 models selected
> select add #5
28445 atoms, 29738 bonds, 3082 residues, 2 models selected
> select subtract #5
24129 atoms, 25314 bonds, 2540 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel light gray
> select #3/K
Nothing selected
> select #10/K
3447 atoms, 3863 bonds, 169 residues, 1 model selected
> select #10/I,J
8632 atoms, 8848 bonds, 1084 residues, 1 model selected
> color sel hot pink
> hide #9 models
> color sel cornflower blue
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #10/I
Alignment identifier is 10/I
> select #10/I:481
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #10/I:481-490
88 atoms, 92 bonds, 10 residues, 1 model selected
> select #5/A:481
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/A:481-490
88 atoms, 92 bonds, 10 residues, 1 model selected
> select #10/I:481
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #10/I:481-490
88 atoms, 92 bonds, 10 residues, 1 model selected
> hide #5 models
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/E,F
2752 atoms, 2802 bonds, 354 residues, 1 model selected
> color sel lime
> select clear
> show #5 models
> hide #10 models
> select #5/A:481
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/A:481-490
88 atoms, 92 bonds, 10 residues, 1 model selected
> show #10 models
> hide #5 models
> select add #5
4316 atoms, 4424 bonds, 542 residues, 1 model selected
> select subtract #5
Nothing selected
> select #10/I:481-482
18 atoms, 19 bonds, 2 residues, 1 model selected
> select #10/I:481-490
88 atoms, 92 bonds, 10 residues, 1 model selected
> show #5 models
> hide #10 models
> select #5/A:481
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/A:481-490
88 atoms, 92 bonds, 10 residues, 1 model selected
> show #10 models
> hide #5 models
> select add #5
4316 atoms, 4424 bonds, 542 residues, 1 model selected
> select subtract #5
Nothing selected
> select #10/I:481
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #10/I:481-490
88 atoms, 92 bonds, 10 residues, 1 model selected
> select #10/I:490-491
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #10
24129 atoms, 25314 bonds, 2540 residues, 1 model selected
> select subtract #10
Nothing selected
> select
> #10/I:59-68,74-80,88-90,92-98,155-172,186-189,191-199,212-235,240-256,260-262,267-272,294-296,349-354,359-372,484-486,490-492,513-523,531-536,538-541
1335 atoms, 1350 bonds, 158 residues, 1 model selected
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #4 models
> hide #10 models
> select add #10
24129 atoms, 25314 bonds, 2540 residues, 1 model selected
> select subtract #10
Nothing selected
> show #1 models
> hide #4 models
> show #!7 models
> hide #!7 models
> show #4 models
> show #10 models
> hide #4 models
> hide #10 models
> hide #1 models
> show #5 models
> show #9 models
> show #10 models
> hide #9 models
> hide #5 models
> show #5 models
> hide #10 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> color #5 #9437ffff
> select #5/A:479-481
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #5/A:479-481
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #5/A:480
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:480-492
116 atoms, 121 bonds, 13 residues, 1 model selected
> color #5 #ff2600ff
> color #5 #531b93ff
> color #5 #9437ffff
> color #5 #d783ffff
> color sel red
> select clear
> show #10 models
> hide #5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #10/I
Alignment identifier is 10/I
> select #10/I:480
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #10/I:480-492
116 atoms, 121 bonds, 13 residues, 1 model selected
> color sel red
> show #5 models
> show #1 models
> hide #1 models
> ui tool show Matchmaker
> matchmaker #10/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain A (#10), sequence
alignment score = 436
RMSD between 102 pruned atom pairs is 0.214 angstroms; (across all 122 pairs:
4.250)
> matchmaker #10/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain A (#10), sequence
alignment score = 436
RMSD between 102 pruned atom pairs is 0.214 angstroms; (across all 122 pairs:
4.250)
> show #1 models
> ui tool show Matchmaker
> matchmaker #10/E to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain E (#10), sequence
alignment score = 93.8
RMSD between 50 pruned atom pairs is 0.979 angstroms; (across all 89 pairs:
14.792)
> matchmaker #10/B to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain B (#10), sequence
alignment score = 436
RMSD between 102 pruned atom pairs is 0.226 angstroms; (across all 122 pairs:
4.155)
> matchmaker #10/B to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain B (#10), sequence
alignment score = 436
RMSD between 102 pruned atom pairs is 0.226 angstroms; (across all 122 pairs:
4.155)
> hide #5 models
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/I
7502 atoms, 7630 bonds, 943 residues, 1 model selected
> color sel orange
> select #10/I
4316 atoms, 4424 bonds, 542 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #5/A to #10/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain I (#10)
with fold_tal1_integrase_long_dimer_model_0.cif, chain A (#5), sequence
alignment score = 2729.1
RMSD between 235 pruned atom pairs is 0.452 angstroms; (across all 542 pairs:
53.406)
> matchmaker #5/A to #10/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain I (#10)
with fold_tal1_integrase_long_dimer_model_0.cif, chain A (#5), sequence
alignment score = 2729.1
RMSD between 235 pruned atom pairs is 0.452 angstroms; (across all 542 pairs:
53.406)
> matchmaker #5/A to #10/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain I (#10)
with fold_tal1_integrase_long_dimer_model_0.cif, chain A (#5), sequence
alignment score = 2729.1
RMSD between 235 pruned atom pairs is 0.452 angstroms; (across all 542 pairs:
53.406)
> hide #1 models
> show #5 models
> select clear
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_evade_int_long_dimer/fold_ch3_nuc_601_evade_int_long_dimer_model_0.cif
Chain information for fold_ch3_nuc_601_evade_int_long_dimer_model_0.cif #11
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K | .
L | .
> select add #11
23779 atoms, 24954 bonds, 2476 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #11/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_evade_int_long_dimer_model_0.cif, chain A (#11), sequence
alignment score = 436
RMSD between 102 pruned atom pairs is 0.193 angstroms; (across all 122 pairs:
4.436)
> matchmaker #11/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_evade_int_long_dimer_model_0.cif, chain A (#11), sequence
alignment score = 436
RMSD between 102 pruned atom pairs is 0.193 angstroms; (across all 122 pairs:
4.436)
> select subtract #11
Nothing selected
> show #1 models
> select add #11
23779 atoms, 24954 bonds, 2476 residues, 1 model selected
> color sel light gray
> select #11/E,F
2752 atoms, 2802 bonds, 354 residues, 1 model selected
> color sel lime
> hide #1 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #5 models
> hide #10 models
> select #11/I,J
8282 atoms, 8488 bonds, 1020 residues, 1 model selected
> color sel magenta
> select clear
> show #10 models
> select #11/I
4141 atoms, 4244 bonds, 510 residues, 1 model selected
> select #10/I
4316 atoms, 4424 bonds, 542 residues, 1 model selected
> select #10/J
4316 atoms, 4424 bonds, 542 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #11/J
4141 atoms, 4244 bonds, 510 residues, 1 model selected
> select #11/I
4141 atoms, 4244 bonds, 510 residues, 1 model selected
> hide sel cartoons
> select #11/J
4141 atoms, 4244 bonds, 510 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #11/J
Alignment identifier is 11/J
> color sel cyan
> select #11/J:455
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #11/J:455-459
49 atoms, 48 bonds, 5 residues, 1 model selected
> select #11/J:460
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/J:455-460
60 atoms, 60 bonds, 6 residues, 1 model selected
> color sel hot pink
> select #11/J:458
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/J:458
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> set bgColor white
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> select #5/A:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> style #10-11 stick
Changed 47908 atom styles
> show #10-11 atoms
> undo
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/I:490
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> lighting full
> select clear
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer_r892k/fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_0.cif
Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_0.cif
#12
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K | .
L | .
> select add #12
24125 atoms, 25310 bonds, 2540 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel light gray
> ui tool show Matchmaker
> matchmaker #12/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_0.cif, chain A (#12),
sequence alignment score = 446.8
RMSD between 102 pruned atom pairs is 0.234 angstroms; (across all 122 pairs:
4.401)
> select subtract #12
Nothing selected
> select add #10
24129 atoms, 25314 bonds, 2540 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #11
23779 atoms, 24954 bonds, 2476 residues, 1 model selected
> select subtract #11
Nothing selected
> hide #11 models
> select #12/J
4314 atoms, 4422 bonds, 542 residues, 1 model selected
> select #12/I
4314 atoms, 4422 bonds, 542 residues, 1 model selected
> select add #12
24125 atoms, 25310 bonds, 2540 residues, 1 model selected
> select subtract #12
Nothing selected
> select add #10
24129 atoms, 25314 bonds, 2540 residues, 1 model selected
> hide #10 models
> select subtract #10
Nothing selected
> select add #12
24125 atoms, 25310 bonds, 2540 residues, 1 model selected
> show #10 models
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer_r892k/fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_1.cif
Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_1.cif
#13
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K | .
L | .
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer_r892k/fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_2.cif
Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_2.cif
#14
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K | .
L | .
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer_r892k/fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_3.cif
Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_3.cif
#15
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K | .
L | .
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer_r892k/fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_4.cif
Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_4.cif
#16
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K | .
L | .
> select subtract #12
Nothing selected
> select add #13
24125 atoms, 25310 bonds, 2540 residues, 1 model selected
> select add #14
48250 atoms, 50620 bonds, 5080 residues, 2 models selected
> select add #15
72375 atoms, 75930 bonds, 7620 residues, 3 models selected
> select add #16
96500 atoms, 101240 bonds, 10160 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #13/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_1.cif, chain A (#13),
sequence alignment score = 437.8
RMSD between 102 pruned atom pairs is 0.222 angstroms; (across all 122 pairs:
4.382)
> matchmaker #14/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_2.cif, chain A (#14),
sequence alignment score = 434.2
RMSD between 102 pruned atom pairs is 0.229 angstroms; (across all 122 pairs:
4.676)
> matchmaker #15/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_3.cif, chain A (#15),
sequence alignment score = 423.4
RMSD between 102 pruned atom pairs is 0.282 angstroms; (across all 122 pairs:
4.897)
> matchmaker #16/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_4.cif, chain A (#16),
sequence alignment score = 436
RMSD between 102 pruned atom pairs is 0.224 angstroms; (across all 122 pairs:
4.142)
> matchmaker #16/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_4.cif, chain A (#16),
sequence alignment score = 436
RMSD between 102 pruned atom pairs is 0.224 angstroms; (across all 122 pairs:
4.142)
> hide #13 models
> hide #14 models
> hide #15 models
> select subtract #13
72375 atoms, 75930 bonds, 7620 residues, 3 models selected
> select subtract #14
48250 atoms, 50620 bonds, 5080 residues, 2 models selected
> select subtract #15
24125 atoms, 25310 bonds, 2540 residues, 1 model selected
> hide #16 models
> select subtract #16
Nothing selected
> show #16 models
> hide #12 models
> show #15 models
> hide #16 models
> ui tool show Matchmaker
> matchmaker #15/B to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_3.cif, chain B (#15),
sequence alignment score = 423.4
RMSD between 102 pruned atom pairs is 0.287 angstroms; (across all 122 pairs:
4.662)
> matchmaker #15/B to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_3.cif, chain B (#15),
sequence alignment score = 423.4
RMSD between 102 pruned atom pairs is 0.287 angstroms; (across all 122 pairs:
4.662)
> show #14 models
> hide #15 models
> show #13 models
> hide #14 models
> show #12 models
> hide #13 models
> show #11 models
> hide #12 models
> hide #11 models
> show #11 models
> hide #10 models
> show #10 models
> show #12 models
> hide #11 models
> show #11 models
> hide #12 models
> hide #10 models
> select #11/A
966 atoms, 978 bonds, 131 residues, 1 model selected
> select #11/A,B
1932 atoms, 1956 bonds, 262 residues, 1 model selected
> color sel red
> hide #11 models
> show #11 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> hide #11 models
> show #10 models
> save
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/AtCENH3-nuc_Tal1_EVADE.cxs
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_h3_nuc_601_tal1_int_long_dimer/fold_h3_nuc_601_tal1_int_long_dimer_model_0.cif
Chain information for fold_h3_nuc_601_tal1_int_long_dimer_model_0.cif #17
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K | .
L | .
> select add #12
26057 atoms, 27266 bonds, 2802 residues, 2 models selected
> select add #11
47904 atoms, 50264 bonds, 5016 residues, 2 models selected
> select subtract #12
23779 atoms, 24954 bonds, 2476 residues, 1 model selected
> select subtract #11
Nothing selected
> select add #17
23509 atoms, 24672 bonds, 2456 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel light gray
> select #11/I,J
8282 atoms, 8488 bonds, 1020 residues, 1 model selected
> close #13-16
> select #17/I,J
8632 atoms, 8848 bonds, 1084 residues, 1 model selected
> color sel hot pink
> select #17/E,F
2132 atoms, 2160 bonds, 270 residues, 1 model selected
> color sel cornflower blue
> ui tool show Matchmaker
No reference and/or match structure/chain chosen
> matchmaker #17/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_h3_nuc_601_tal1_int_long_dimer_model_0.cif, chain A (#17), sequence
alignment score = 441.4
RMSD between 102 pruned atom pairs is 0.238 angstroms; (across all 122 pairs:
4.370)
> select clear
> select #17/J
4316 atoms, 4424 bonds, 542 residues, 1 model selected
> select #17/I
4316 atoms, 4424 bonds, 542 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #17/B:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> open
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_h3_nuc_601_evade_int_long_dimer/fold_h3_nuc_601_evade_int_long_dimer_model_0.cif
Chain information for fold_h3_nuc_601_evade_int_long_dimer_model_0.cif #13
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K | .
L | .
> select add #17
23509 atoms, 24672 bonds, 2456 residues, 1 model selected
> select add #13
46668 atoms, 48984 bonds, 4848 residues, 2 models selected
> select subtract #17
23159 atoms, 24312 bonds, 2392 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel light gray
> ui tool show Matchmaker
> matchmaker #13/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with
fold_h3_nuc_601_evade_int_long_dimer_model_0.cif, chain A (#13), sequence
alignment score = 450.4
RMSD between 102 pruned atom pairs is 0.222 angstroms; (across all 122 pairs:
4.421)
> show #11 models
> hide #10 models
> hide #17 models
> select #13/I
4141 atoms, 4244 bonds, 510 residues, 1 model selected
> hide sel cartoons
> select #13/A,B
1932 atoms, 1956 bonds, 262 residues, 1 model selected
> hide #11 models
> show #11 models
> select add #13
23159 atoms, 24312 bonds, 2392 residues, 1 model selected
> select subtract #13
Nothing selected
> hide #11 models
> show #11 models
> hide #13 models
> select #13/A,B
1932 atoms, 1956 bonds, 262 residues, 1 model selected
> select #11/A,B
1932 atoms, 1956 bonds, 262 residues, 1 model selected
> color sel light gray
> select clear
> show #13 models
> select #11/E,F
2752 atoms, 2802 bonds, 354 residues, 1 model selected
> color sel cornflower blue
> show #17 models
> hide #11 models
> select add #11
23779 atoms, 24954 bonds, 2476 residues, 1 model selected
> select subtract #11
Nothing selected
> hide #17 models
> show #17 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> select #11/E,F
2752 atoms, 2802 bonds, 354 residues, 1 model selected
> color #13,17 lime
> show #11 models
> hide #13 models
> hide #17 models
> undo
[Repeated 7 time(s)]
> hide #17 models
> hide #13 models
> show #13 models
> show #11 models
> hide #13 models
> show #10 models
> hide #11 models
> show #11 models
> select #11/E,F
2752 atoms, 2802 bonds, 354 residues, 1 model selected
> color sel lime
> hide #10 models
> hide #11 models
> show #11 models
> select clear
> show #12 models
> hide #11 models
> show #11 models
> hide #11 models
> show #13 models
> hide #12 models
> select #13/E,F
2132 atoms, 2160 bonds, 270 residues, 1 model selected
> color sel cornflower blue
> select #17/E,F
2132 atoms, 2160 bonds, 270 residues, 1 model selected
> color #13 cornflower blue
> show #17 models
> hide #17 models
> select #17/E,F
2132 atoms, 2160 bonds, 270 residues, 1 model selected
> show #17 models
> hide #13 models
> show #13 models
> hide #17 models
> select add #17
23509 atoms, 24672 bonds, 2456 residues, 1 model selected
> select subtract #17
Nothing selected
> select #13
23159 atoms, 24312 bonds, 2392 residues, 1 model selected
> color sel light gray
> select #13/E,F
2132 atoms, 2160 bonds, 270 residues, 1 model selected
> color sel cornflower blue
> select add #13
23159 atoms, 24312 bonds, 2392 residues, 1 model selected
> select subtract #13
Nothing selected
> show #17 models
> hide #13 models
> show #13 models
> hide #17 models
> select #13/I
4141 atoms, 4244 bonds, 510 residues, 1 model selected
> select #13/J
4141 atoms, 4244 bonds, 510 residues, 1 model selected
> color sel orange
> show #17 models
> select add #13
23159 atoms, 24312 bonds, 2392 residues, 1 model selected
> select subtract #13
Nothing selected
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> show #12 models
> hide #13 models
> hide #12 models
> show #10 models
> show #13 models
> show #9 models
> hide #17 models
> hide #10 models
> hide #9 models
> show #11 models
> show #17 models
> hide #17 models
> save
> /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/AtCENH3-nuc_Tal1_EVADE.cxs
——— End of log from Tue Jul 2 13:03:40 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11C000D7J/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 2分 2秒
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2419HC:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 16 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Qt fatal error: Failed to initialize graphics backend for OpenGL |
comment:2 by , 16 months ago
Note:
See TracTickets
for help on using tickets.
Although we see Qt fail to initialize OpenGL often on Linux, it is rare to see it on a Mac. No idea what causes the problem. The use had two displays. Mac M1 GPU. I'd guess it has something to do with the buggy Mac Qt handling of multiple displays.