![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8643 closed defect (nonchimerax)
Graphics crash, macOS 12.5, Intel HD Graphics 615
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x0000000113456600 (most recent call first):
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 497 in swap_buffers
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 191 in draw
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 2300000,
"procLaunch" : "2023-03-14 22:38:54.9957 +1300",
"procRole" : "Foreground",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBook10,1",
"procStartAbsTime" : 2330094904971053,
"coalitionID" : 159756,
"osVersion" : {
"train" : "macOS 12.5",
"build" : "21G72",
"releaseType" : "User"
},
"captureTime" : "2023-03-14 23:27:22.0245 +1300",
"incident" : "663F06BF-35FF-4D1E-978A-890374E21A5F",
"bug_type" : "309",
"pid" : 25486,
"procExitAbsTime" : 2333001844804294,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/programs\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0AFD1FF8-1FCD-55A8-86C9-F5E7FF42CB53","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F9DE9519-8F67-2FD4-4503-3567FAA55CDA",
"wakeTime" : 3404,
"sleepWakeUUID" : "0448E770-959D-48AE-A318-3A505E6D5D82",
"sip" : "enabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/SZ3_NTd.pdb
Chain information for SZ3_NTd.pdb #1
---
Chain | Description
A | No description available
> set bgColor white
> hide atoms
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/Omicron_7wk2_NTD.pdb
Omicron_7wk2_NTD.pdb title:
Sars-cov-2 ο S-close [more info...]
Chain information for Omicron_7wk2_NTD.pdb #2
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2
> ui tool show "Side View"
> ui mousemode right select
Drag select of 262 residues, 4 pseudobonds
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-88.011,0,1,0,31.72,0,0,1,-59.275
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.17893,0.6391,-0.74802,164.13,0.88075,-0.44288,-0.16771,110.08,-0.43847,-0.62882,-0.64213,522.2
> view matrix models
> #2,0.14547,0.7139,-0.68497,145.07,0.86987,-0.42212,-0.25522,128.41,-0.47134,-0.55871,-0.68241,526.69
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.14547,0.7139,-0.68497,136.99,0.86987,-0.42212,-0.25522,128.2,-0.47134,-0.55871,-0.68241,521.34
> view matrix models
> #2,0.14547,0.7139,-0.68497,136.09,0.86987,-0.42212,-0.25522,126.33,-0.47134,-0.55871,-0.68241,518.64
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SZ3_NTd.pdb, chain A (#1) with Omicron_7wk2_NTD.pdb, chain A (#2),
sequence alignment score = 3227.6
RMSD between 197 pruned atom pairs is 1.020 angstroms; (across all 254 pairs:
2.394)
> select add #2
2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected
> select subtract #2
Nothing selected
> hide #1 models
> show #1 models
> select add #1
4346 atoms, 4423 bonds, 294 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium sea green
> select subtract #1
Nothing selected
> select add #2
2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light salmon
> color sel salmon
> color sel dark salmon
> color sel maroon
> color sel coral
> color sel light salmon
> color sel salmon
> color sel peach puff
> color sel moccasin
> color sel wheat
> color sel pale goldenrod
> color sel tan
> color sel burly wood
> color sel tan
> select subtract #2
Nothing selected
> lighting full
> save /Users/bostinalab/Desktop/image1.png supersample 3
> select add #2
2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected
> close #2
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/RatG13_NTD.pdb
RatG13_NTD.pdb title:
Cryo-em structure of bat RATG13 spike glycoprotein [more info...]
Chain information for RatG13_NTD.pdb #2
---
Chain | Description
A | spike glycoprotein
Non-standard residues in RatG13_NTD.pdb #2
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> select add #2
2208 atoms, 2268 bonds, 296 residues, 1 model selected
> view matrix models #2,1,0,0,17.045,0,1,0,-29.042,0,0,1,31.335
> view matrix models #2,1,0,0,15.734,0,1,0,-21.689,0,0,1,33.355
> view matrix models #2,1,0,0,-6.2958,0,1,0,58.452,0,0,1,29.721
> hide sel atoms
> view matrix models #2,1,0,0,-4.4385,0,1,0,50.95,0,0,1,29.382
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.66957,-0.73116,0.1307,113.51,0.7427,0.65699,-0.12946,26.866,0.0087865,0.18375,0.98293,6.3096
> view matrix models
> #2,0.91886,-0.37728,0.11555,39.074,0.18245,0.1466,-0.97222,279.64,0.34986,0.91442,0.20354,-21.553
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.91886,-0.37728,0.11555,68.734,0.18245,0.1466,-0.97222,291.49,0.34986,0.91442,0.20354,-46.995
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.94227,-0.32695,0.072373,65.348,0.075,-0.0045842,-0.99717,327.82,0.32636,0.94503,0.020202,-22.485
> view matrix models
> #2,0.053025,0.98311,-0.17514,31.226,-0.97437,0.012539,-0.22461,341.05,-0.21862,0.18256,0.95858,11.37
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.053025,0.98311,-0.17514,30.448,-0.97437,0.012539,-0.22461,353.9,-0.21862,0.18256,0.95858,21.573
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SZ3_NTd.pdb, chain A (#1) with RatG13_NTD.pdb, chain A (#2),
sequence alignment score = 3364.1
RMSD between 208 pruned atom pairs is 0.835 angstroms; (across all 273 pairs:
2.911)
> ui tool show "Color Actions"
> color sel tan
> select subtract #2
Nothing selected
> save /Users/bostinalab/Desktop/image2.png supersample 3
> close #2
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/pCoV-GX_NTD.pdb
pCoV-GX_NTD.pdb title:
Structure of coronavirus spike from smuggled guangdong pangolin [more info...]
Chain information for pCoV-GX_NTD.pdb #2
---
Chain | Description
A | surface glycoprotein
Non-standard residues in pCoV-GX_NTD.pdb #2
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> ui mousemode right select
Drag select of 145 atoms, 249 residues, 4 pseudobonds, 140 bonds
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-28.344,0,1,0,-2.6339,0,0,1,-101.95
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.73959,0.44457,-0.50533,56.112,-0.44722,0.8857,0.12466,108.83,0.50299,0.13379,0.85387,-227.05
> view matrix models
> #2,-0.99928,-0.010959,0.036423,477.74,-0.0016656,0.96928,0.24595,-53.366,-0.038,0.24571,-0.9686,322.11
> show sel cartoons
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SZ3_NTd.pdb, chain A (#1) with pCoV-GX_NTD.pdb, chain A (#2),
sequence alignment score = 3332.9
RMSD between 230 pruned atom pairs is 0.748 angstroms; (across all 243 pairs:
1.525)
> ui tool show "Color Actions"
> color sel tan
> select add #2
2081 atoms, 2140 bonds, 4 pseudobonds, 255 residues, 2 models selected
> select subtract #2
Nothing selected
> save /Users/bostinalab/Desktop/image3.png supersample 3
> close #2
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/MERS_8h15_NTD.pdb
MERS_8h15_NTD.pdb title:
Structure of sars-cov-1 spike protein (S/native) At pH 5.5, closed
conformation [more info...]
Chain information for MERS_8h15_NTD.pdb #2
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS
Non-standard residues in MERS_8h15_NTD.pdb #2
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> select add #2
1638 atoms, 1680 bonds, 6 pseudobonds, 202 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-12.307,0,1,0,22.159,0,0,1,-20.132
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.75167,0.25014,-0.61027,91.758,0.61867,-0.58807,0.52098,122.23,-0.22856,-0.76916,-0.59679,447.82
> view matrix models
> #2,0.43594,-0.88488,-0.16414,245.87,-0.74728,-0.45755,0.48189,281.73,-0.50152,-0.087417,-0.86072,413.76
> view matrix models
> #2,0.20459,-0.95149,-0.22979,299.61,-0.85821,-0.28726,0.42538,276.93,-0.47076,0.11018,-0.87536,378.08
> view matrix models
> #2,0.35485,-0.92051,-0.16352,262.35,-0.79548,-0.38917,0.46451,279.26,-0.49122,-0.034753,-0.87034,405.07
> view matrix models
> #2,0.3263,-0.93196,0.15806,206.81,-0.84453,-0.21231,0.49162,249.48,-0.42461,-0.2939,-0.85635,439.15
> view matrix models
> #2,0.81914,-0.57065,0.058148,99.618,-0.40378,-0.50165,0.76506,191.58,-0.4074,-0.65016,-0.64133,458.28
> view matrix models
> #2,-0.065096,-0.99623,-0.057345,309.12,-0.9294,0.039608,0.36693,239.79,-0.36328,0.077182,-0.92848,379.92
> view matrix models
> #2,0.47974,-0.85826,-0.18232,239.06,-0.76483,-0.51089,0.39245,310.3,-0.42998,-0.048828,-0.90152,405.26
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.47974,-0.85826,-0.18232,238.31,-0.76483,-0.51089,0.39245,312.03,-0.42998,-0.048828,-0.90152,404.41
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SZ3_NTd.pdb, chain A (#1) with MERS_8h15_NTD.pdb, chain A (#2),
sequence alignment score = 4096.2
RMSD between 200 pruned atom pairs is 0.627 angstroms; (across all 200 pairs:
0.627)
> ui tool show "Color Actions"
> color sel tan
> show sel cartoons
> hide sel atoms
> select subtract #2
Nothing selected
> save /Users/bostinalab/Desktop/image4.png supersample 3
> close #2
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/Delta_7e7b_NTD.pdb
Delta_7e7b_NTD.pdb title:
Cryo-em structure of the sars-cov-2 furin site mutant S-trimer from A subunit
vaccine candidate [more info...]
Chain information for Delta_7e7b_NTD.pdb #2
---
Chain | Description | UniProt
A | spike glycoprotein,collagen α-1(I) chain | CO1A1_HUMAN
Non-standard residues in Delta_7e7b_NTD.pdb #2
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
VCG — 2-hydroxyethyl
2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-α-L-
xylo-hexofuranoside (polysorbate 80)
> ui mousemode right select
> select add #2
2391 atoms, 2452 bonds, 1 pseudobond, 299 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-27.694,0,1,0,60.065,0,0,1,-34.737
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.71067,0.50688,-0.48787,53.084,0.50537,-0.85025,-0.14722,193.95,-0.48944,-0.14193,-0.86041,386.72
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.71067,0.50688,-0.48787,46.065,0.50537,-0.85025,-0.14722,237.96,-0.48944,-0.14193,-0.86041,407.73
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SZ3_NTd.pdb, chain A (#1) with Delta_7e7b_NTD.pdb, chain A (#2),
sequence alignment score = 3406.6
RMSD between 249 pruned atom pairs is 0.745 angstroms; (across all 273 pairs:
1.875)
> show sel cartoons
> hide sel atoms
> ui tool show "Color Actions"
> color sel tan
> select subtract #2
Nothing selected
> save /Users/bostinalab/Desktop/image1.png supersample 3
> select add #2
2391 atoms, 2452 bonds, 1 pseudobond, 299 residues, 2 models selected
> close #2
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/007_NTD.pdb
Chain information for 007_NTD.pdb #2
---
Chain | Description
A | No description available
> select add #2
4369 atoms, 4447 bonds, 293 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-19.003,0,1,0,23.715,0,0,1,-41.963
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.090444,-0.75393,0.6507,228.03,0.99558,-0.085068,0.039816,5.6637,0.025336,0.65143,0.75829,-121.75
> view matrix models
> #2,-0.0683,-0.98884,0.13242,364.14,-0.064925,0.13685,0.98846,10.006,-0.99555,0.058914,-0.073547,359.23
> view matrix models
> #2,-0.32415,0.941,-0.097203,103.9,0.89793,0.33839,0.28146,-98.614,0.29775,0.0039552,-0.95464,261.59
> view matrix models
> #2,-0.67218,0.72759,-0.13707,224.33,0.6864,0.6818,0.253,-111.58,0.27754,0.075979,-0.95771,252.94
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.67218,0.72759,-0.13707,218.07,0.6864,0.6818,0.253,-93.373,0.27754,0.075979,-0.95771,249.85
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SZ3_NTd.pdb, chain A (#1) with 007_NTD.pdb, chain A (#2), sequence
alignment score = 4343.5
RMSD between 272 pruned atom pairs is 0.384 angstroms; (across all 274 pairs:
0.435)
> show sel cartoons
> hide sel atoms
> ui tool show "Color Actions"
> color sel royal blue
> select subtract #2
Nothing selected
> save /Users/bostinalab/Desktop/image2.png supersample 3
> close #1
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/Omicron_7wk2_NTD.pdb
Omicron_7wk2_NTD.pdb title:
Sars-cov-2 ο S-close [more info...]
Chain information for Omicron_7wk2_NTD.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2
> select add #1
2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-32.84,0,1,0,1.5395,0,0,1,-113.37
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.82808,0.53442,0.16932,279.85,0.15038,-0.079214,0.98545,-61.996,0.54006,0.8415,-0.014771,-169.25
> view matrix models
> #1,-0.17644,-0.61087,-0.77182,532.42,0.26919,-0.78417,0.55912,128.3,-0.94679,-0.10912,0.3028,290.63
> view matrix models
> #1,0.33381,-0.74421,-0.57856,389.11,0.30611,-0.49492,0.81324,11.85,-0.89155,-0.44857,0.062602,390.47
> view matrix models
> #1,0.42993,-0.62416,-0.65237,360.79,-0.029238,-0.7318,0.68089,164.69,-0.90239,-0.27366,-0.33287,449.64
> view matrix models
> #1,0.68177,0.15386,-0.7152,175.62,0.59552,-0.68455,0.42042,61.947,-0.4249,-0.71255,-0.55833,461.09
> view matrix models
> #1,0.33644,0.86183,-0.37955,59.976,0.90797,-0.18996,0.3735,-91.293,0.24979,-0.47028,-0.84643,317.77
> view matrix models
> #1,-0.22747,0.97344,0.025795,87.717,0.80395,0.17278,0.56904,-173.5,0.54947,0.15018,-0.82191,129.53
> view matrix models
> #1,-0.351,0.92809,-0.12429,159.02,0.69546,0.34727,0.62907,-191.3,0.627,0.13436,-0.76735,101.39
> view matrix models
> #1,-0.22126,0.95418,-0.20144,139.91,0.71089,0.29922,0.63648,-188.18,0.66759,-0.0023724,-0.74452,110.68
> view matrix models
> #1,-0.33458,0.93629,-0.10688,149.72,0.6709,0.31631,0.6707,-189.05,0.66178,0.1527,-0.73399,82.298
> view matrix models
> #1,-0.50751,0.84444,0.17131,146.5,0.63764,0.23436,0.73382,-180.41,0.57952,0.48166,-0.65739,27.099
> view matrix models
> #1,-0.74934,0.64824,0.13516,248.1,0.42683,0.31679,0.84703,-168.77,0.50626,0.69241,-0.51408,-24.116
> view matrix models
> #1,-0.92644,0.3752,-0.030558,376.22,0.10568,0.33714,0.9355,-113.81,0.3613,0.86346,-0.35199,-55.011
> view matrix models
> #1,-0.91865,-0.061635,0.39023,358.57,0.3755,0.17078,0.91095,-144.56,-0.12279,0.98338,-0.13374,-6.7586
> view matrix models
> #1,-0.28509,-0.57684,-0.76549,551.43,0.28838,-0.81325,0.50543,140.66,-0.91409,-0.07666,0.3982,255.81
> view matrix models
> #1,0.12426,0.01403,-0.99215,397.33,0.61438,-0.78626,0.065828,153.84,-0.77916,-0.61774,-0.10632,430.46
> view matrix models
> #1,-0.40577,0.90318,0.14006,118.26,0.88334,0.3482,0.31378,-167.4,0.23464,0.25104,-0.93911,214.21
> view matrix models
> #1,-0.38532,0.918,0.093884,120.88,0.89399,0.34614,0.28455,-163.16,0.22872,0.19357,-0.95405,229.13
> view matrix models
> #1,-0.58454,0.80005,-0.13505,240.91,0.47891,0.47457,0.73853,-185.37,0.65495,0.36702,-0.66055,29.748
> view matrix models
> #1,-0.41084,0.89317,-0.18294,192.75,0.22758,0.29477,0.92807,-134.32,0.88285,0.33965,-0.32437,-95.256
> view matrix models
> #1,-0.3,0.93789,-0.17427,155.94,0.044498,0.19624,0.97954,-83.712,0.9529,0.2861,-0.10061,-152.34
> view matrix models
> #1,-0.49624,0.74396,-0.44751,298.51,-0.24579,0.37398,0.89427,-25.686,0.83267,0.55377,-0.0027288,-192.15
> view matrix models
> #1,-0.5245,0.59026,-0.61359,369.36,-0.41998,0.44753,0.78951,26.857,0.74062,0.6718,0.013169,-194.17
> view matrix models
> #1,-0.41355,-0.098647,-0.90512,528.89,-0.89948,0.19835,0.38936,276.22,0.14112,0.97516,-0.17076,-61.325
> view matrix models
> #1,-0.51942,-0.7,-0.49011,569.32,-0.22035,-0.44443,0.86829,118.83,-0.82562,0.559,0.0766,192.87
> view matrix models
> #1,-0.96273,0.053506,0.26514,376.59,0.2635,0.40673,0.87472,-151.08,-0.061037,0.91198,-0.40567,51.041
> view matrix models
> #1,-0.31911,0.90538,0.2801,65.791,0.94024,0.26539,0.21335,-144.35,0.11883,0.33144,-0.93596,227.45
> view matrix models
> #1,-0.1197,0.98421,0.13042,36.432,0.9922,0.11399,0.050439,-94.127,0.034776,0.13544,-0.99017,294.62
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.1197,0.98421,0.13042,39.838,0.9922,0.11399,0.050439,-54.151,0.034776,0.13544,-0.99017,326.01
> ui tool show Matchmaker
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 007_NTD.pdb, chain A (#2) with Omicron_7wk2_NTD.pdb, chain A (#1),
sequence alignment score = 3234.6
RMSD between 201 pruned atom pairs is 1.032 angstroms; (across all 254 pairs:
2.404)
> view matrix models
> #1,-0.10665,0.99095,0.081562,-22.046,0.99326,0.10993,-0.036854,-45.216,-0.045486,0.077081,-0.99599,371.45
> undo
> select subtract #1
Nothing selected
> select add #1
2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected
> ui tool show "Color Actions"
> color sel tan
> select subtract #1
Nothing selected
> save /Users/bostinalab/Desktop/image1.png supersample 3
> select add #1
2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected
> close #1
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/RatG13_NTD.pdb
RatG13_NTD.pdb title:
Cryo-em structure of bat RATG13 spike glycoprotein [more info...]
Chain information for RatG13_NTD.pdb #1
---
Chain | Description
A | spike glycoprotein
Non-standard residues in RatG13_NTD.pdb #1
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> select add #1
2208 atoms, 2268 bonds, 296 residues, 1 model selected
> view matrix models #1,1,0,0,-7.5996,0,1,0,50.432,0,0,1,22.015
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98776,0.12219,0.096912,-36.031,-0.042506,0.80879,-0.58655,163.43,-0.15006,0.57526,0.80409,-9.1085
> view matrix models
> #1,0.98643,0.13039,0.099784,-37.373,-0.042009,0.78794,-0.61431,170.05,-0.15872,0.60178,0.78273,-8.6395
> view matrix models
> #1,-0.60328,0.66753,0.43643,31.999,-0.7482,-0.28423,-0.59951,394.13,-0.27614,-0.6882,0.67091,192.53
> view matrix models
> #1,0.091113,0.95401,0.28561,-67.067,-0.78866,0.24424,-0.56424,323.68,-0.60804,-0.17384,0.77464,148.82
> view matrix models
> #1,0.66664,0.73438,0.12761,-83.752,-0.5514,0.60106,-0.57852,250.16,-0.50155,0.3153,0.80562,66.814
> view matrix models
> #1,0.58538,0.80778,0.069472,-75.714,-0.63703,0.51126,-0.57689,272.01,-0.50152,0.29345,0.81386,68.557
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.58538,0.80778,0.069472,-78.682,-0.63703,0.51126,-0.57689,286.7,-0.50152,0.29345,0.81386,69.649
> ui tool show Matchmaker
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 007_NTD.pdb, chain A (#2) with RatG13_NTD.pdb, chain A (#1),
sequence alignment score = 3358.5
RMSD between 209 pruned atom pairs is 0.808 angstroms; (across all 274 pairs:
2.841)
> show sel cartoons
> hide sel atoms
> ui tool show "Color Actions"
> color sel tan
> select subtract #1
Nothing selected
> save /Users/bostinalab/Desktop/image2.png supersample 3
> select add #1
2208 atoms, 2268 bonds, 296 residues, 1 model selected
> close #1
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/pCoV-GX_NTD.pdb
pCoV-GX_NTD.pdb title:
Structure of coronavirus spike from smuggled guangdong pangolin [more info...]
Chain information for pCoV-GX_NTD.pdb #1
---
Chain | Description
A | surface glycoprotein
Non-standard residues in pCoV-GX_NTD.pdb #1
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> select add #1
2081 atoms, 2140 bonds, 4 pseudobonds, 255 residues, 2 models selected
> view matrix models #1,1,0,0,-11.465,0,1,0,4.2934,0,0,1,-74.44
> ui tool show Matchmaker
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 007_NTD.pdb, chain A (#2) with pCoV-GX_NTD.pdb, chain A (#1),
sequence alignment score = 3334.7
RMSD between 233 pruned atom pairs is 0.737 angstroms; (across all 244 pairs:
1.488)
> show sel cartoons
> hide sel atoms
> ui tool show "Color Actions"
> color sel tan
> select subtract #1
Nothing selected
> save /Users/bostinalab/Desktop/image3.png supersample 3
> select add #1
2081 atoms, 2140 bonds, 4 pseudobonds, 255 residues, 2 models selected
> close #1
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/MERS_8h15_NTD.pdb
MERS_8h15_NTD.pdb title:
Structure of sars-cov-1 spike protein (S/native) At pH 5.5, closed
conformation [more info...]
Chain information for MERS_8h15_NTD.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS
Non-standard residues in MERS_8h15_NTD.pdb #1
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> select add #1
1638 atoms, 1680 bonds, 6 pseudobonds, 202 residues, 2 models selected
> view matrix models #1,1,0,0,-10.393,0,1,0,29.188,0,0,1,-29.546
> show sel cartoons
> hide sel atoms
> ui tool show "Color Actions"
> color sel tan
> ui tool show Matchmaker
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 007_NTD.pdb, chain A (#2) with MERS_8h15_NTD.pdb, chain A (#1),
sequence alignment score = 4116.9
RMSD between 200 pruned atom pairs is 0.620 angstroms; (across all 200 pairs:
0.620)
> select subtract #1
Nothing selected
> save /Users/bostinalab/Desktop/image4.png supersample 3
> select add #1
1638 atoms, 1680 bonds, 6 pseudobonds, 202 residues, 2 models selected
> close #1
> open /Users/bostinalab/Documents/PDBs/Mine/NTDs/Delta_7e7b_NTD.pdb
Delta_7e7b_NTD.pdb title:
Cryo-em structure of the sars-cov-2 furin site mutant S-trimer from A subunit
vaccine candidate [more info...]
Chain information for Delta_7e7b_NTD.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein,collagen α-1(I) chain | CO1A1_HUMAN
Non-standard residues in Delta_7e7b_NTD.pdb #1
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
VCG — 2-hydroxyethyl
2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-α-L-
xylo-hexofuranoside (polysorbate 80)
> ui tool show Matchmaker
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 007_NTD.pdb, chain A (#2) with Delta_7e7b_NTD.pdb, chain A (#1),
sequence alignment score = 3409.6
RMSD between 252 pruned atom pairs is 0.696 angstroms; (across all 274 pairs:
1.747)
> show cartoons
> hide atoms
> save /Users/bostinalab/Desktop/image5.png supersample 3
> select add #1
2391 atoms, 2452 bonds, 1 pseudobond, 299 residues, 2 models selected
> select add #2
6760 atoms, 6899 bonds, 1 pseudobond, 592 residues, 3 models selected
> close #2
> close #1
> open /Users/bostinalab/Documents/PDBs/Mine/RBDs/SZ3_RBD.pdb
Chain information for SZ3_RBD.pdb #1
---
Chain | Description
A | No description available
> open /Users/bostinalab/Documents/PDBs/Mine/RBDs/Omicron_7wk2_RBD.pdb
Omicron_7wk2_RBD.pdb title:
Sars-cov-2 ο S-close [more info...]
Chain information for Omicron_7wk2_RBD.pdb #2
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2
> select add #2
1793 atoms, 1848 bonds, 223 residues, 1 model selected
> select add #1
4791 atoms, 4894 bonds, 419 residues, 2 models selected
> select subtract #2
2998 atoms, 3046 bonds, 196 residues, 1 model selected
> view matrix models #1,1,0,0,30.055,0,1,0,63.687,0,0,1,0
> view matrix models #1,1,0,0,36.716,0,1,0,46.825,0,0,1,107.3
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SZ3_RBD.pdb, chain A (#1) with Omicron_7wk2_RBD.pdb, chain A (#2),
sequence alignment score = 3127.6
RMSD between 165 pruned atom pairs is 1.161 angstroms; (across all 194 pairs:
2.162)
> view matrix models #1,1,0,0,36.795,0,1,0,46.581,0,0,1,108.68
> close #1
> open /Users/bostinalab/Downloads/Complete_SZ3.pdb
Chain information for Complete_SZ3.pdb #1
---
Chain | Description
A B C | No description available
> select #1/A
16663 atoms, 16899 bonds, 3 pseudobonds, 1132 residues, 2 models selected
> select ~sel
35119 atoms, 35646 bonds, 6 pseudobonds, 2487 residues, 3 models selected
> select subtract #2
33326 atoms, 33798 bonds, 6 pseudobonds, 2264 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> show cartoons
> hide atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:292
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/A:3-292
4316 atoms, 4381 bonds, 290 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:517
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:517-1106
8284 atoms, 8365 bonds, 3 pseudobonds, 570 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select add #1
4063 atoms, 4146 bonds, 272 residues, 1 model selected
> view matrix models #1,1,0,0,3.3905,0,1,0,26.834,0,0,1,35.241
> view matrix models #1,1,0,0,4.0703,0,1,0,54.603,0,0,1,97.953
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Complete_SZ3.pdb, chain A (#1) with Omicron_7wk2_RBD.pdb, chain A
(#2), sequence alignment score = 3146.2
RMSD between 193 pruned atom pairs is 1.161 angstroms; (across all 222 pairs:
2.060)
> ui tool show "Color Actions"
> color sel medium sea green
> select add #2
5856 atoms, 5994 bonds, 495 residues, 2 models selected
> select subtract #1
1793 atoms, 1848 bonds, 223 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tan
> select subtract #2
Nothing selected
> save /Users/bostinalab/Desktop/image1.png supersample 3
> select add #2
1793 atoms, 1848 bonds, 223 residues, 1 model selected
> close #2
> open /Users/bostinalab/Documents/PDBs/Mine/RBDs/007_RBD.pdb
Chain information for 007_RBD.pdb #2
---
Chain | Description
A | No description available
> select add #2
3496 atoms, 3558 bonds, 229 residues, 1 model selected
> close #2
> open /Users/bostinalab/Downloads/Complete_007.pdb
Chain information for Complete_007.pdb #2
---
Chain | Description
A B C | No description available
Undo failed, probably because structures have been modified.
> select #2/A
16438 atoms, 16677 bonds, 3 pseudobonds, 1116 residues, 2 models selected
> select ~sel
36939 atoms, 37500 bonds, 6 pseudobonds, 2504 residues, 3 models selected
> select subtract #1
32876 atoms, 33354 bonds, 6 pseudobonds, 2232 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:291-292
34 atoms, 34 bonds, 2 residues, 1 model selected
> select #2/A:3-292
4378 atoms, 4445 bonds, 290 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A:517-519
40 atoms, 39 bonds, 3 residues, 1 model selected
> select #2/A:517-1107
8251 atoms, 8335 bonds, 3 pseudobonds, 574 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select add #2
3809 atoms, 3882 bonds, 252 residues, 1 model selected
> view matrix models #2,1,0,0,-15.776,0,1,0,-35.006,0,0,1,-7.8099
> ui mousemode right select
> select subtract #2
Nothing selected
Drag select of 273 atoms, 283 bonds
> delete atoms sel
> delete bonds sel
Drag select of 39 atoms, 41 bonds
> delete atoms sel
> delete bonds sel
> select add #2
3497 atoms, 3558 bonds, 230 residues, 1 model selected
> show sel cartoons
> hide sel atoms
Drag select of 10 residues
> select add #2
3497 atoms, 3558 bonds, 230 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,57.536,0,1,0,21.875,0,0,1,22.87
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Complete_SZ3.pdb, chain A (#1) with Complete_007.pdb, chain A (#2),
sequence alignment score = 4243.9
RMSD between 224 pruned atom pairs is 0.309 angstroms; (across all 224 pairs:
0.309)
> view matrix models
> #2,-0.77186,0.63578,0.0036126,194.05,0.63576,0.77187,-0.004394,-11.781,-0.0055821,-0.0010948,-0.99998,436.66
> undo
> ui tool show "Side View"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.8.4
OpenGL renderer: Intel(R) HD Graphics 615
OpenGL vendor: Intel Inc.
Python: 3.9.11
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
Model Identifier: MacBook10,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 451.140.1.0.0
OS Loader Version: 540.120.3~19
SMC Version (system): 2.42f13
Software:
System Software Overview:
System Version: macOS 12.5 (21G72)
Kernel Version: Darwin 21.6.0
Time since boot: 94 days 4:05
Graphics/Displays:
Intel HD Graphics 615:
Chipset Model: Intel HD Graphics 615
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x591e
Revision ID: 0x0002
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2304 x 1440 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
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: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 12.5, Intel HD Graphics 615 |
Apple Intel graphics driver crash.
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