![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 23 months ago
Closed 23 months ago
#10311 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020234a240 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 110000,
"procRole" : "Background",
"version" : 2,
"userID" : 1017607982,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 3823,
"osVersion" : {
"train" : "macOS 14.1.2",
"build" : "23B92",
"releaseType" : "User"
},
"captureTime" : "2023-12-08 15:55:02.4712 -0500",
"codeSigningMonitor" : 1,
"incident" : "49C73472-CA3D-41A3-B529-7E0AB5154A05",
"pid" : 45014,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-12-07 14:34:43.3407 -0500",
"procStartAbsTime" : 2090788308509,
"procExitAbsTime" : 2753970897736,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8AFF4201-4A10-51A1-B835-88BF60316D32","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "96201331-C3C7-15E8-F049-ECD45751791F",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 2,
"sleepWakeUUID" : "7ECB2B7F-C87F-4E67-B506-5D2FE25805B9",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140722904334312\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc9ab98000-7ffcc0240000 [598.7M] r-x\/r-x SM=COW ...t_id=9cea4dc1",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":45014},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140722904334312\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc9ab98000-7ffcc0240000 [598.7M] r-x\/r-x SM=COW ...t_id=9cea4dc1",
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"faultingThread" : 0,
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"name" : "libsystem_c.dylib"
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"size" : 40960,
"uuid" : "c94f952c-2787-30d2-ab77-ee474abd88d6",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
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"arch" : "x86_64",
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"size" : 4820989,
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
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"size" : 12840956,
"uuid" : "581d66fd-7cef-3a8c-8647-1d962624703b",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
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"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 20996092,
"uuid" : "27fed5dd-d148-3238-bc95-1dac5dd57fa1",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
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"uuid" : "14809357-5d5a-3255-9cd2-ec5bc50f24cb",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
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"size" : 290814,
"uuid" : "4472f1a5-1d47-3665-ac8d-7adb0e9d2d87",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
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"logWritingSignature" : "1d8d67bf46e6d5923d0a770e9f41195b4dc59339",
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{
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"PC register does not match crashing frame (0x0 vs 0x7FF8969C6A78)"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/mortonaj/Downloads/cryosparc_P5_J143_volume_map_consensus.mrc
Opened cryosparc_P5_J143_volume_map_consensus.mrc as #1, grid size 72,72,72,
pixel 3.47, shown at level 0.0637, step 1, values float32
> open /Users/mortonaj/Downloads/1gfl.pdb
1gfl.pdb title:
Structure of green fluorescent protein [more info...]
Chain information for 1gfl.pdb #2
---
Chain | Description | UniProt
A B | green fluorescent protein | GFP_AEQVI 1-238
> hide #!1 models
> show #!1 models
> select add #2
3950 atoms, 3738 bonds, 760 residues, 1 model selected
> volume #1 level 0.3275
> ui tool show "Fit in Map"
> select subtract #2
Nothing selected
> select add #2
3950 atoms, 3738 bonds, 760 residues, 1 model selected
> hide #2 models
> select subtract #2
Nothing selected
> open /Users/mortonaj/Downloads/4kw4.pdb
4kw4.pdb title:
Crystal structure of green fluorescent protein [more info...]
Chain information for 4kw4.pdb #3
---
Chain | Description | UniProt
A | green fluorescent protein | GFP_AEQVI 2-238
Non-standard residues in 4kw4.pdb #3
---
CRO —
{2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid (peptide derived chromophore)
> ui mousemode right "translate selected models"
> select add #3
3792 atoms, 3535 bonds, 531 residues, 1 model selected
> view matrix models #3,1,0,0,29.917,0,1,0,89.337,0,0,1,124.12
> view matrix models #3,1,0,0,89.408,0,1,0,56.445,0,0,1,133.53
> view matrix models #3,1,0,0,89.745,0,1,0,88.101,0,0,1,99.678
> ui tool show "Fit in Map"
> view matrix models #3,1,0,0,132.96,0,1,0,85.174,0,0,1,150.12
> view matrix models #3,1,0,0,94.965,0,1,0,92.232,0,0,1,107.84
> view matrix models #3,1,0,0,106.53,0,1,0,80.825,0,0,1,101.78
> ui tool show "Fit in Map"
> view matrix models #3,1,0,0,89.28,0,1,0,92.804,0,0,1,114.31
> view matrix models #3,1,0,0,99.296,0,1,0,86.165,0,0,1,106.81
> fitmap #2 inMap #1
Fit molecule 1gfl.pdb (#2) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3950 atoms
average map value = 0.009378, steps = 1720
shifted from previous position = 18.2
rotated from previous position = 48.7 degrees
atoms outside contour = 3950, contour level = 0.32754
Position of 1gfl.pdb (#2) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
0.94987865 -0.03017608 -0.31115904 -7.22573234
-0.19997947 0.70639054 -0.67898499 24.69424020
0.24028891 0.70717877 0.66495070 -62.88536428
Axis 0.92321143 -0.36727482 -0.11309228
Axis point 0.00000000 87.41489087 -6.09831907
Rotation angle (degrees) 48.65359292
Shift along axis -8.62860182
> view matrix models #3,1,0,0,115.87,0,1,0,90.412,0,0,1,106.25
> fitmap #2 inMap #1
Fit molecule 1gfl.pdb (#2) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3950 atoms
average map value = 0.009438, steps = 2000
shifted from previous position = 0.089
rotated from previous position = 0.286 degrees
atoms outside contour = 3950, contour level = 0.32754
Position of 1gfl.pdb (#2) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
0.94999959 -0.02724042 -0.31106065 -7.40303844
-0.20089784 0.70930193 -0.67567065 24.59201137
0.23904148 0.70437825 0.66836401 -62.71785246
Axis 0.92263931 -0.36777382 -0.11609963
Axis point 0.00000000 87.63807455 -5.98594781
Rotation angle (degrees) 48.40715920
Shift along axis -8.59311282
> fitmap #3 inMap #1
Fit molecule 4kw4.pdb (#3) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3792 atoms
average map value = 0.4857, steps = 196
shifted from previous position = 6.1
rotated from previous position = 91.4 degrees
atoms outside contour = 916, contour level = 0.32754
Position of 4kw4.pdb (#3) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
-0.01691492 0.18238464 0.98308175 115.93536290
-0.01744699 0.98301888 -0.18267316 90.09377621
-0.99970470 -0.02024172 -0.01344563 115.00666741
Axis 0.08123849 0.99167109 -0.09994381
Axis point 115.20164915 0.00000000 8.44731477
Rotation angle (degrees) 91.35636555
Shift along axis 87.26760131
> volume #1 level 0.1437
> volume #1 level 0.4254
> volume #1 level 0.3394
> view matrix models
> #3,-0.016915,0.18238,0.98308,115.91,-0.017447,0.98302,-0.18267,88.087,-0.9997,-0.020242,-0.013446,118.06
> fitmap #3 inMap #1
Fit molecule 4kw4.pdb (#3) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3792 atoms
average map value = 0.4857, steps = 64
shifted from previous position = 3.66
rotated from previous position = 0.164 degrees
atoms outside contour = 1000, contour level = 0.3394
Position of 4kw4.pdb (#3) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
-0.01923554 0.18398126 0.98274152 115.88528705
-0.01777328 0.98270514 -0.18432233 90.12800328
-0.99965699 -0.02101208 -0.01563291 115.04298239
Axis 0.08168291 0.99153656 -0.10091160
Axis point 115.07303078 0.00000000 8.67549926
Rotation angle (degrees) 91.49453827
Shift along axis 87.22188697
> volume #1 level 0.06366
> volume #1 level 0.1882
> volume #1 level 0.3098
> volume #1 level 0.6626
> volume #1 level 0.4669
> volume #1 level 0.4788
> volume #1 level 0.1111
> fitmap #3 inMap #1
Fit molecule 4kw4.pdb (#3) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3792 atoms
average map value = 0.4857, steps = 48
shifted from previous position = 0.0561
rotated from previous position = 0.139 degrees
atoms outside contour = 198, contour level = 0.1111
Position of 4kw4.pdb (#3) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
-0.02045479 0.18232904 0.98302478 115.99418407
-0.01654076 0.98303421 -0.18267496 90.07770095
-0.99965394 -0.01999655 -0.01709190 114.98512628
Axis 0.08136944 0.99170780 -0.09947185
Axis point 114.97780766 0.00000000 8.58734541
Rotation angle (degrees) 91.56186069
Shift along axis 87.33135647
> volume #1 level 0.07255
> fitmap #3 inMap #1
Fit molecule 4kw4.pdb (#3) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3792 atoms
average map value = 0.4857, steps = 28
shifted from previous position = 0.0514
rotated from previous position = 0.212 degrees
atoms outside contour = 140, contour level = 0.072554
Position of 4kw4.pdb (#3) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
-0.02062583 0.18554800 0.98241871 115.85269399
-0.01820003 0.98239524 -0.18592567 90.14517516
-0.99962160 -0.02171492 -0.01688573 115.06822884
Axis 0.08213657 0.99139668 -0.10191272
Axis point 115.00567313 0.00000000 8.83937027
Rotation angle (degrees) 91.57916622
Shift along axis 87.15845447
> volume #1 level 0.2445
> volume #1 level 0.4995
> volume #1 level 0.1912
> volume #1 level 0.2475
> volume #1 level 0.8257
> open /Users/mortonaj/Downloads/5c6r.pdb
5c6r.pdb title:
Crystal structure of pH domain of ASAP1 [more info...]
Chain information for 5c6r.pdb #4
---
Chain | Description | UniProt
A B | arf-gap | ASAP1_MOUSE 325-451
Non-standard residues in 5c6r.pdb #4
---
PGE — triethylene glycol
PO4 — phosphate ion
> view matrix models
> #3,-0.020626,0.18555,0.98242,117.5,-0.0182,0.9824,-0.18593,94.744,-0.99962,-0.021715,-0.016886,119.09
> select subtract #3
Nothing selected
> hide #2 target m
> select add #4
1831 atoms, 1822 bonds, 257 residues, 1 model selected
> view matrix models #4,1,0,0,75.02,0,1,0,80.885,0,0,1,133.33
> view matrix models #4,1,0,0,139.93,0,1,0,164.9,0,0,1,150.86
> hide #4 models
> open /Users/mortonaj/Downloads/5c6r.pdb1.gz
Summary of feedback from opening /Users/mortonaj/Downloads/5c6r.pdb1.gz
---
warnings | Start residue of secondary structure not found: HELIX 3 AA3 LEU B
386 CYS B 388 5 3
Start residue of secondary structure not found: HELIX 4 AA4 ASP B 415 GLY B
440 1 26
Start residue of secondary structure not found: SHEET 1 AA2 7 ALA B 381 ASN B
384 0
Start residue of secondary structure not found: SHEET 2 AA2 7 ILE B 368 ILE B
371 -1 N LEU B 369 O LEU B 383
Start residue of secondary structure not found: SHEET 3 AA2 7 TRP B 357 LYS B
365 -1 N ALA B 363 O THR B 370
4 messages similar to the above omitted
5c6r.pdb1.gz title:
Crystal structure of pH domain of ASAP1 [more info...]
Chain information for 5c6r.pdb1.gz #5
---
Chain | Description
A | No description available
Non-standard residues in 5c6r.pdb1.gz #5
---
PGE — triethylene glycol
PO4 — phosphate ion
> select add #5
2773 atoms, 2755 bonds, 391 residues, 2 models selected
> view matrix models
> #4,1,0,0,297.9,0,1,0,199.28,0,0,1,204.92,#5,1,0,0,157.97,0,1,0,34.381,0,0,1,54.061
> view matrix models
> #4,1,0,0,241.69,0,1,0,268.14,0,0,1,257.95,#5,1,0,0,101.76,0,1,0,103.23,0,0,1,107.09
> volume #1 level 0.3631
> ui mousemode right translate
> ui mousemode right "translate selected models"
> select subtract #4
942 atoms, 933 bonds, 134 residues, 1 model selected
> select add #3
4734 atoms, 4468 bonds, 665 residues, 2 models selected
> view matrix models
> #3,-0.020626,0.18555,0.98242,199.37,-0.0182,0.9824,-0.18593,134.46,-0.99962,-0.021715,-0.016886,134.42,#5,1,0,0,183.63,0,1,0,142.96,0,0,1,122.42
> select subtract #3
942 atoms, 933 bonds, 134 residues, 1 model selected
> view matrix models #5,1,0,0,210.58,0,1,0,125.94,0,0,1,145.02
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.82704,-0.069818,0.5578,210.42,-0.51868,0.28782,0.80506,134.71,-0.21675,-0.95514,0.20182,160.78
> ui mousemode right "translate selected models"
> select add #3
4734 atoms, 4468 bonds, 665 residues, 2 models selected
> view matrix models
> #3,-0.020626,0.18555,0.98242,145.13,-0.0182,0.9824,-0.18593,75.824,-0.99962,-0.021715,-0.016886,100.39,#5,0.82704,-0.069818,0.5578,156.18,-0.51868,0.28782,0.80506,76.07,-0.21675,-0.95514,0.20182,126.74
> view matrix models
> #3,-0.020626,0.18555,0.98242,118.33,-0.0182,0.9824,-0.18593,92.457,-0.99962,-0.021715,-0.016886,115.2,#5,0.82704,-0.069818,0.5578,129.38,-0.51868,0.28782,0.80506,92.703,-0.21675,-0.95514,0.20182,141.55
> fitmap #5 inMap #1
Fit molecule 5c6r.pdb1.gz (#5) to map
cryosparc_P5_J143_volume_map_consensus.mrc (#1) using 942 atoms
average map value = 0.5751, steps = 112
shifted from previous position = 36.5
rotated from previous position = 52.2 degrees
atoms outside contour = 179, contour level = 0.36312
Position of 5c6r.pdb1.gz (#5) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
0.88013244 0.47468883 0.00611575 118.75313346
-0.36992184 0.67769345 0.63552295 112.09189467
0.29753104 -0.56160672 0.77205775 110.85690399
Axis -0.80140409 -0.19508447 -0.56541448
Axis point 0.00000000 54.44622146 -93.59784250
Rotation angle (degrees) 48.32213800
Shift along axis -179.71673319
> select subtract #5
3792 atoms, 3535 bonds, 531 residues, 1 model selected
> view matrix models
> #3,-0.020626,0.18555,0.98242,161,-0.0182,0.9824,-0.18593,26.383,-0.99962,-0.021715,-0.016886,54.248
> volume #1 level 0.704
> volume #1 level 0.1633
> hide #!1 models
> show #!1 models
> view matrix models
> #3,-0.020626,0.18555,0.98242,186.63,-0.0182,0.9824,-0.18593,59.683,-0.99962,-0.021715,-0.016886,86.975
> view matrix models
> #3,-0.020626,0.18555,0.98242,190.44,-0.0182,0.9824,-0.18593,80.284,-0.99962,-0.021715,-0.016886,102.14
> view matrix models
> #3,-0.020626,0.18555,0.98242,117.35,-0.0182,0.9824,-0.18593,86.357,-0.99962,-0.021715,-0.016886,140.48
> view matrix models
> #3,-0.020626,0.18555,0.98242,112.18,-0.0182,0.9824,-0.18593,78.222,-0.99962,-0.021715,-0.016886,122.48
> volume #1 level 0.3073
> ui mousemode right translate
> ui mousemode right "translate selected models"
> volume #1 level 0.2838
> volume #1 step 4
> volume #1 level 0.3171
> volume #1 level 0.198
> volume #1 step 2
> volume #1 step 1
> volume #1 style mesh
> volume #1 level 0.1539
> open /Users/mortonaj/Downloads/emd_9277.map.gz
File reader requires uncompressed file;
'/Users/mortonaj/Downloads/emd_9277.map.gz' is compressed
> open /Users/mortonaj/Downloads/emd_9277.map
Opened emd_9277.map as #6, grid size 360,360,360, pixel 0.831, shown at level
0.00287, step 2, values float32
> select subtract #3
Nothing selected
> select add #6
2 models selected
> view matrix models #6,1,0,0,43.784,0,1,0,76.198,0,0,1,0.51923
> select add #4
1831 atoms, 1822 bonds, 257 residues, 3 models selected
> select subtract #4
2 models selected
> select add #3
3792 atoms, 3535 bonds, 531 residues, 3 models selected
> view matrix models
> #3,-0.020626,0.18555,0.98242,103.05,-0.0182,0.9824,-0.18593,84.273,-0.99962,-0.021715,-0.016886,119.73,#6,1,0,0,34.647,0,1,0,82.249,0,0,1,-2.2295
> select subtract #6
3792 atoms, 3535 bonds, 531 residues, 1 model selected
> view matrix models
> #3,-0.020626,0.18555,0.98242,157.55,-0.0182,0.9824,-0.18593,162.44,-0.99962,-0.021715,-0.016886,213.59
> view matrix models
> #3,-0.020626,0.18555,0.98242,133.09,-0.0182,0.9824,-0.18593,199.56,-0.99962,-0.021715,-0.016886,194.77
> fitmap #3 inMap #6
Fit molecule 4kw4.pdb (#3) to map emd_9277.map (#6) using 3792 atoms
average map value = 0.002975, steps = 364
shifted from previous position = 8.99
rotated from previous position = 25.6 degrees
atoms outside contour = 1811, contour level = 0.0028738
Position of 4kw4.pdb (#3) relative to emd_9277.map (#6) coordinates:
Matrix rotation and translation
0.18851133 0.17684145 0.96601790 102.23539697
-0.39318951 0.91496624 -0.09076776 124.19502985
-0.89992527 -0.36271736 0.24201371 213.22514114
Axis -0.13805018 0.94721152 -0.28936567
Axis point 201.78668537 0.00000000 57.69895122
Rotation angle (degrees) 80.05250500
Shift along axis 41.82531168
> hide #!6 models
> open /Users/mortonaj/Downloads/6mwq.pdb1.gz
Summary of feedback from opening /Users/mortonaj/Downloads/6mwq.pdb1.gz
---
warnings | Start residue of secondary structure not found: HELIX 26 AC8 ASP B
27 GLY B 39 1 13
Start residue of secondary structure not found: HELIX 27 AC9 GLN B 40 GLY B 51
1 12
Start residue of secondary structure not found: HELIX 28 AD1 THR B 63 ARG B 71
1 9
Start residue of secondary structure not found: HELIX 29 AD2 HIS B 73 LEU B 81
1 9
Start residue of secondary structure not found: HELIX 30 AD3 THR B 96 ALA B
102 1 7
156 messages similar to the above omitted
6mwq.pdb1.gz title:
Single particle cryoem structure of A darpin-aldolase platform In complex with
GFP [more info...]
Chain information for 6mwq.pdb1.gz #7
---
Chain | Description
A | No description available
G | No description available
> view matrix models
> #3,0.18851,0.17684,0.96602,98.356,-0.39319,0.91497,-0.090768,180.69,-0.89993,-0.36272,0.24201,132.92
> select add #5
4734 atoms, 4468 bonds, 665 residues, 2 models selected
> view matrix models
> #3,0.18851,0.17684,0.96602,38.207,-0.39319,0.91497,-0.090768,185.7,-0.89993,-0.36272,0.24201,30.307,#5,0.88013,0.47469,0.0061158,58.603,-0.36992,0.67769,0.63552,117.1,0.29753,-0.56161,0.77206,8.2463
> select subtract #3
942 atoms, 933 bonds, 134 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #7
5524 atoms, 5627 bonds, 719 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-20.719,0,1,0,11.318,0,0,1,-7.1178
> fitmap #7 inMap #1
Fit molecule 6mwq.pdb1.gz (#7) to map
cryosparc_P5_J143_volume_map_consensus.mrc (#1) using 5524 atoms
average map value = 0.1689, steps = 480
shifted from previous position = 19.8
rotated from previous position = 52.8 degrees
atoms outside contour = 3432, contour level = 0.15394
Position of 6mwq.pdb1.gz (#7) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
0.64853124 0.40055168 -0.64727551 91.74079541
-0.17016493 0.90511985 0.38961771 4.21992440
0.74192394 -0.14253567 0.65515834 -45.14670130
Axis -0.33398296 -0.87187071 -0.35818550
Axis point 104.71008670 0.00000000 75.51233089
Rotation angle (degrees) 52.81398229
Shift along axis -18.14819759
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.64853,0.40055,-0.64728,2.9709,-0.17016,0.90512,0.38962,-44.647,0.74192,-0.14254,0.65516,-80.239
> view matrix models
> #7,0.64853,0.40055,-0.64728,8.1788,-0.17016,0.90512,0.38962,-50.72,0.74192,-0.14254,0.65516,-62.808
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.30477,-0.81856,0.48689,130.25,-0.77192,0.51175,0.37717,87.142,-0.5579,-0.26089,-0.78783,353.21
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.30477,-0.81856,0.48689,133.71,-0.77192,0.51175,0.37717,126.31,-0.5579,-0.26089,-0.78783,322.66
> view matrix models
> #7,-0.30477,-0.81856,0.48689,173.8,-0.77192,0.51175,0.37717,128.2,-0.5579,-0.26089,-0.78783,301.02
> view matrix models
> #7,-0.30477,-0.81856,0.48689,173.38,-0.77192,0.51175,0.37717,132.91,-0.5579,-0.26089,-0.78783,302.18
> hide #7 models
> select subtract #7
Nothing selected
> select add #5
942 atoms, 933 bonds, 134 residues, 1 model selected
> view matrix models
> #5,0.88013,0.47469,0.0061158,38.853,-0.36992,0.67769,0.63552,127.87,0.29753,-0.56161,0.77206,89.021
> select add #3
4734 atoms, 4468 bonds, 665 residues, 2 models selected
> view matrix models
> #3,0.18851,0.17684,0.96602,35.166,-0.39319,0.91497,-0.090768,176.48,-0.89993,-0.36272,0.24201,34.278,#5,0.88013,0.47469,0.0061158,35.812,-0.36992,0.67769,0.63552,118.65,0.29753,-0.56161,0.77206,92.992
> select subtract #5
3792 atoms, 3535 bonds, 531 residues, 1 model selected
> view matrix models
> #3,0.18851,0.17684,0.96602,100.07,-0.39319,0.91497,-0.090768,103.35,-0.89993,-0.36272,0.24201,109.43
> select subtract #3
Nothing selected
> select add #5
942 atoms, 933 bonds, 134 residues, 1 model selected
> view matrix models
> #5,0.88013,0.47469,0.0061158,91.883,-0.36992,0.67769,0.63552,64.924,0.29753,-0.56161,0.77206,119.04
> select subtract #5
Nothing selected
> select add #3
3792 atoms, 3535 bonds, 531 residues, 1 model selected
> view matrix models
> #3,0.18851,0.17684,0.96602,107,-0.39319,0.91497,-0.090768,98.527,-0.89993,-0.36272,0.24201,123.25
> view matrix models
> #3,0.18851,0.17684,0.96602,109.44,-0.39319,0.91497,-0.090768,92.542,-0.89993,-0.36272,0.24201,120.85
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.53916,-0.54438,0.64262,130.74,0.45554,0.83027,0.32114,85.082,-0.70837,0.11959,0.69563,101.35
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.53916,-0.54438,0.64262,133.82,0.45554,0.83027,0.32114,95.816,-0.70837,0.11959,0.69563,97.779
> select subtract #3
Nothing selected
> select add #5
942 atoms, 933 bonds, 134 residues, 1 model selected
> view matrix models
> #5,0.88013,0.47469,0.0061158,117.54,-0.36992,0.67769,0.63552,94.813,0.29753,-0.56161,0.77206,123.72
> view matrix models
> #5,0.88013,0.47469,0.0061158,120.74,-0.36992,0.67769,0.63552,89.777,0.29753,-0.56161,0.77206,126.82
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.53606,0.53005,-0.65703,114.8,0.68324,-0.18469,-0.70645,109.76,-0.4958,-0.82761,-0.26315,129.12
> view matrix models
> #5,0.64973,0.50346,-0.56955,119.96,0.75313,-0.52804,0.39238,114.51,-0.1032,-0.68389,-0.72225,128.84
> view matrix models
> #5,0.7363,0.40195,-0.54433,121.96,0.66853,-0.55644,0.4934,114.53,-0.10457,-0.7272,-0.67842,129.5
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.7363,0.40195,-0.54433,121.39,0.66853,-0.55644,0.4934,117.69,-0.10457,-0.7272,-0.67842,131.37
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.90934,-0.40974,0.072233,127.43,0.31175,-0.78599,-0.53389,121.16,0.27553,-0.46297,0.84246,126.89
> view matrix models
> #5,-0.83118,-0.49849,0.24627,129.02,-0.04984,-0.37434,-0.92595,113.32,0.55376,-0.78191,0.2863,133.9
> view matrix models
> #5,-0.29726,0.081617,0.9513,120.84,0.045198,-0.99402,0.099406,122.82,0.95373,0.072546,0.2918,121.41
> view matrix models
> #5,0.62667,-0.064807,0.77659,127.21,0.29655,-0.90173,-0.31455,122.77,0.72066,0.42741,-0.54587,115.52
> view matrix models
> #5,-0.26135,0.71337,0.65023,110.89,-0.91313,-0.40108,0.073018,109.16,0.31289,-0.57466,0.75622,128.98
> view matrix models
> #5,0.13074,-0.87946,-0.45767,139.99,0.36018,0.47222,-0.80454,100.88,0.92368,-0.059662,0.3785,123.37
> view matrix models
> #5,0.094923,-0.90371,-0.41749,140.2,0.36748,0.42157,-0.829,101.77,0.92518,-0.074726,0.37211,123.64
> view matrix models
> #5,-0.32771,0.35688,0.87478,116.26,-0.50018,-0.85105,0.15982,118.17,0.80152,-0.38517,0.4574,128.17
> view matrix models
> #5,0.065256,-0.15171,0.98627,126.13,-0.34691,-0.93017,-0.12013,120.41,0.93562,-0.33431,-0.11333,128.49
> view matrix models
> #5,0.39967,-0.30846,0.8632,130.21,-0.45856,-0.88266,-0.10309,119.15,0.79372,-0.35462,-0.49422,128.67
> view matrix models
> #5,0.61162,-0.43756,0.65913,133.43,-0.54155,-0.83891,-0.054392,118.04,0.57675,-0.32368,-0.75006,127.56
> view matrix models
> #5,0.49586,-0.38428,0.77875,131.95,-0.29192,-0.91834,-0.26728,120.6,0.81787,-0.094796,-0.56755,124.56
> view matrix models
> #5,0.3012,-0.24927,0.9204,128.77,-0.22971,-0.95577,-0.18368,121.38,0.92548,-0.1561,-0.34514,125.76
> ui mousemode right zoom
> ui mousemode right translate
> fitmap #4 inMap #1
Fit molecule 5c6r.pdb (#4) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 1831 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1831, contour level = 0.15394
Position of 5c6r.pdb (#4) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 241.68649111
0.00000000 1.00000000 0.00000000 268.13578655
0.00000000 0.00000000 1.00000000 257.94840156
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 257.94840156
> fitmap #4 inMap #1
Fit molecule 5c6r.pdb (#4) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 1831 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1831, contour level = 0.15394
Position of 5c6r.pdb (#4) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 241.68649111
0.00000000 1.00000000 0.00000000 268.13578655
0.00000000 0.00000000 1.00000000 257.94840156
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 257.94840156
> fitmap #3 inMap #1
Fit molecule 4kw4.pdb (#3) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3792 atoms
average map value = 0.4857, steps = 172
shifted from previous position = 10.3
rotated from previous position = 61.1 degrees
atoms outside contour = 271, contour level = 0.15394
Position of 4kw4.pdb (#3) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
-0.01903143 0.18171186 0.98316764 116.01219626
-0.01622044 0.98316021 -0.18202447 90.05195220
-0.99968730 -0.01941160 -0.01576349 114.95235286
Axis 0.08133355 0.99175805 -0.09899915
Axis point 115.03930302 0.00000000 8.46467454
Rotation angle (degrees) 91.47938998
Shift along axis 87.36524655
> ui mousemode right zoom
> ui mousemode right translate
> select add #3
4734 atoms, 4468 bonds, 665 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.019031,0.18171,0.98317,116.15,-0.01622,0.98316,-0.18202,96.101,-0.99969,-0.019412,-0.015763,111.81,#5,0.3012,-0.24927,0.9204,128.91,-0.22971,-0.95577,-0.18368,127.43,0.92548,-0.1561,-0.34514,122.62
> fitmap #3 inMap #1
Fit molecule 4kw4.pdb (#3) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3792 atoms
average map value = 0.4857, steps = 56
shifted from previous position = 6.81
rotated from previous position = 0.229 degrees
atoms outside contour = 268, contour level = 0.15394
Position of 4kw4.pdb (#3) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
-0.02186231 0.18424183 0.98263777 115.93364261
-0.01726682 0.98265650 -0.18462950 90.11055378
-0.99961187 -0.02100345 -0.01830187 115.02793611
Axis 0.08184687 0.99153480 -0.10079600
Axis point 114.91678140 0.00000000 8.78857439
Rotation angle (degrees) 91.64770040
Shift along axis 87.24219943
> view matrix models
> #3,-0.021862,0.18424,0.98264,112.05,-0.017267,0.98266,-0.18463,91.92,-0.99961,-0.021003,-0.018302,108.08,#5,0.3012,-0.24927,0.9204,125.03,-0.22971,-0.95577,-0.18368,129.24,0.92548,-0.1561,-0.34514,115.68
> view matrix models
> #3,-0.021862,0.18424,0.98264,140.15,-0.017267,0.98266,-0.18463,94.615,-0.99961,-0.021003,-0.018302,152.64,#5,0.3012,-0.24927,0.9204,153.13,-0.22971,-0.95577,-0.18368,131.93,0.92548,-0.1561,-0.34514,160.24
> view matrix models
> #3,-0.021862,0.18424,0.98264,124.63,-0.017267,0.98266,-0.18463,93.59,-0.99961,-0.021003,-0.018302,171.37,#5,0.3012,-0.24927,0.9204,137.61,-0.22971,-0.95577,-0.18368,130.91,0.92548,-0.1561,-0.34514,178.96
> fitmap #3 inMap #1
Fit molecule 4kw4.pdb (#3) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3792 atoms
average map value = 0.4686, steps = 72
shifted from previous position = 10.2
rotated from previous position = 43.2 degrees
atoms outside contour = 242, contour level = 0.15394
Position of 4kw4.pdb (#3) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
0.62240231 -0.03194407 0.78204536 116.96486739
-0.12107661 0.98321020 0.13652162 93.84960446
-0.77327603 -0.17965877 0.60808462 166.98754254
Axis -0.19890126 0.97841419 -0.05607108
Axis point 243.97067790 0.00000000 -46.82118665
Rotation angle (degrees) 52.63801922
Shift along axis 59.19615424
> select subtract #3
942 atoms, 933 bonds, 134 residues, 1 model selected
> view matrix models
> #5,0.3012,-0.24927,0.9204,126.26,-0.22971,-0.95577,-0.18368,102.9,0.92548,-0.1561,-0.34514,140.07
> open /Users/mortonaj/Downloads/4kw4.pdb
4kw4.pdb title:
Crystal structure of green fluorescent protein [more info...]
Chain information for 4kw4.pdb #8
---
Chain | Description | UniProt
A | green fluorescent protein | GFP_AEQVI 2-238
Non-standard residues in 4kw4.pdb #8
---
CRO —
{2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid (peptide derived chromophore)
> select add #8
4734 atoms, 4468 bonds, 665 residues, 2 models selected
> ui mousemode right zoom
> select subtract #5
3792 atoms, 3535 bonds, 531 residues, 1 model selected
> ui mousemode right "move picked models"
> view matrix models #8,1,0,0,103.61,0,1,0,94.174,0,0,1,120.56
> view matrix models #8,1,0,0,114.21,0,1,0,85.603,0,0,1,107.91
> fitmap #8 inMap #1
Fit molecule 4kw4.pdb (#8) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3792 atoms
average map value = 0.4857, steps = 204
shifted from previous position = 8.08
rotated from previous position = 91.4 degrees
atoms outside contour = 268, contour level = 0.15394
Position of 4kw4.pdb (#8) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
-0.01848860 0.18295128 0.98294812 115.91998803
-0.01736906 0.98290903 -0.18327070 90.10754434
-0.99967819 -0.02046131 -0.01499492 115.01633627
Axis 0.08143074 0.99163025 -0.10019221
Axis point 115.10404047 0.00000000 8.56459318
Rotation angle (degrees) 91.44900706
Shift along axis 87.26907641
> ui mousemode right zoom
> ui mousemode right distance
> select subtract #8
Nothing selected
> ui mousemode right distance
> ui mousemode right "tape measure"
> marker segment #9 position 131.3,132.2,136.6 toPosition 134.8,113.8,122.5
> color yellow radius 0.8667 label 23.43 labelHeight 2.343 labelColor yellow
> select add #9
2 atoms, 1 bond, 2 residues, 2 models selected
> marker segment #9 position 135.1,120.4,126.8 toPosition 135.1,126.1,125.3
> color yellow radius 0.8667 label 5.887 labelHeight 1.733 labelColor yellow
> undo
> ui mousemode right select
> select subtract #8
Nothing selected
> select add #9
4 atoms, 2 bonds, 4 residues, 2 models selected
> hide #!9 models
> hide #9.1 models
> volume #6 level 0.005821
> close #6
> volume #1 level 0.1973
> volume #1 level 0.2349
> volume #1 step 16
> volume #1 step 8
> volume #1 step 4
> volume #1 level 0.1435
> volume #1 step 2
> volume #1 level 0.2454
> ui mousemode right "tape measure"
> marker segment #9 position 127.7,126.3,132.1 toPosition 132.8,117.6,127.3
> color yellow radius 0.8667 label 11.24 labelHeight 1.733 labelColor yellow
> ui mousemode right "tape measure"
> marker segment #9 position 129.9,123,133.7 toPosition 123,119.8,123.3 color
> yellow radius 0.8667 label 12.85 labelHeight 1.733 labelColor yellow
> marker delete #9
> ui mousemode right "tape measure"
> marker segment #6 position 122.9,128.3,132.4 toPosition 136.6,118.8,122.8
> color yellow radius 0.8667 label 19.21 labelHeight 1.921 labelColor yellow
> hide #6.1 models
> hide #!6 models
> marker segment #6 position 129.9,123,133.7 toPosition 135.2,125.7,129.5
> color yellow radius 0.8667 label 7.278 labelHeight 1.733 labelColor yellow
> marker segment #6 position 135.2,126.5,131.4 toPosition 121.3,115.3,127.5
> color yellow radius 0.8667 label 18.24 labelHeight 1.824 labelColor yellow
> ui mousemode right "tape measure"
> marker segment #6 position 129.9,123,133.7 toPosition 121.3,115.3,126.8
> color yellow radius 0.8667 label 13.47 labelHeight 1.733 labelColor yellow
> marker segment #6 position 123,122.8,134 toPosition 123,120,123.5 color
> yellow radius 0.8667 label 10.84 labelHeight 1.733 labelColor yellow
> show #!6 models
> show #6.1 models
> hide #6.1 models
> hide #!6 models
> select add #5
942 atoms, 933 bonds, 134 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.3012,-0.24927,0.9204,121.87,-0.22971,-0.95577,-0.18368,119.42,0.92548,-0.1561,-0.34514,125.76
> view matrix models
> #5,0.3012,-0.24927,0.9204,129.11,-0.22971,-0.95577,-0.18368,121.79,0.92548,-0.1561,-0.34514,122.53
> select add #3
4734 atoms, 4468 bonds, 665 residues, 2 models selected
> select subtract #3
942 atoms, 933 bonds, 134 residues, 1 model selected
> select add #8
4734 atoms, 4468 bonds, 665 residues, 2 models selected
> view matrix models
> #5,0.3012,-0.24927,0.9204,128.68,-0.22971,-0.95577,-0.18368,127.61,0.92548,-0.1561,-0.34514,120.61,#8,-0.018489,0.18295,0.98295,115.48,-0.017369,0.98291,-0.18327,95.929,-0.99968,-0.020461,-0.014995,113.09
> view matrix models
> #5,0.3012,-0.24927,0.9204,128.59,-0.22971,-0.95577,-0.18368,125.96,0.92548,-0.1561,-0.34514,121.33,#8,-0.018489,0.18295,0.98295,115.4,-0.017369,0.98291,-0.18327,94.281,-0.99968,-0.020461,-0.014995,113.81
> select subtract #8
942 atoms, 933 bonds, 134 residues, 1 model selected
> view matrix models
> #5,0.3012,-0.24927,0.9204,130.2,-0.22971,-0.95577,-0.18368,122.65,0.92548,-0.1561,-0.34514,125.42
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.066354,-0.0026505,0.99779,125.09,-0.72288,-0.68943,0.04624,116,0.68778,-0.72435,-0.047662,133.51
> view matrix models
> #5,-0.038327,-0.81553,0.57744,138.54,-0.53218,-0.47244,-0.70255,114.01,0.84576,-0.33423,-0.4159,128.11
> view matrix models
> #5,0.81405,-0.52865,-0.24052,138.17,-0.24627,-0.68924,0.6814,117.24,-0.526,-0.49546,-0.69126,125.5
> view matrix models
> #5,0.61866,0.21509,-0.75564,125.66,0.74851,-0.4536,0.48371,117.61,-0.23872,-0.86486,-0.44162,132.5
> select subtract #5
Nothing selected
> select add #3
3792 atoms, 3535 bonds, 531 residues, 1 model selected
> view matrix models
> #3,0.61937,-0.033677,0.78438,117.05,-0.097167,0.98811,0.11915,93.445,-0.77906,-0.15001,0.60873,166.04
> view matrix models
> #3,-0.94819,-0.23592,0.2128,142.74,-0.19165,0.95892,0.20917,95.341,-0.25341,0.15755,-0.95444,152.52
> view matrix models
> #3,-0.93606,-0.35162,0.012666,146.93,-0.35153,0.93307,-0.076185,98.565,0.01497,-0.075766,-0.99701,157.54
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.93606,-0.35162,0.012666,141.81,-0.35153,0.93307,-0.076185,100.65,0.01497,-0.075766,-0.99701,165.84
> fitmap #8 inMap #1
Fit molecule 4kw4.pdb (#8) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3792 atoms
average map value = 0.4857, steps = 72
shifted from previous position = 4.38
rotated from previous position = 0.172 degrees
atoms outside contour = 519, contour level = 0.24535
Position of 4kw4.pdb (#8) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
-0.02140862 0.18352417 0.98278205 115.91518903
-0.01705412 0.98279728 -0.18389852 90.10968116
-0.99962534 -0.02069750 -0.01791049 115.04383914
Axis 0.08163312 0.99159976 -0.10032922
Axis point 114.93285476 0.00000000 8.75330057
Rotation angle (degrees) 91.61944692
Shift along axis 87.27299770
> fitmap #3 inMap #1
Fit molecule 4kw4.pdb (#3) to map cryosparc_P5_J143_volume_map_consensus.mrc
(#1) using 3792 atoms
average map value = 0.4673, steps = 172
shifted from previous position = 7.98
rotated from previous position = 138 degrees
atoms outside contour = 590, contour level = 0.24535
Position of 4kw4.pdb (#3) relative to
cryosparc_P5_J143_volume_map_consensus.mrc (#1) coordinates:
Matrix rotation and translation
-0.18125339 0.20715759 -0.96137035 123.75656860
0.84059570 -0.47475341 -0.26078357 133.83098582
-0.51043715 -0.85539168 -0.08808512 187.59207843
Axis -0.60745705 -0.46067745 0.64712612
Axis point 124.32706063 156.79210425 0.00000000
Rotation angle (degrees) 150.69727048
Shift along axis -15.43398298
> show #!6 models
> show #6.1 models
> hide #6.1 models
> hide #!6 models
> volume #1 level 0.0884
> select add #8
7584 atoms, 7070 bonds, 1062 residues, 2 models selected
> view matrix models
> #3,-0.18125,0.20716,-0.96137,122.66,0.8406,-0.47475,-0.26078,140.63,-0.51044,-0.85539,-0.088085,184.05,#8,-0.021409,0.18352,0.98278,114.82,-0.017054,0.9828,-0.1839,96.911,-0.99963,-0.020697,-0.01791,111.5
> select subtract #8
3792 atoms, 3535 bonds, 531 residues, 1 model selected
> view matrix models
> #3,-0.18125,0.20716,-0.96137,123.62,0.8406,-0.47475,-0.26078,133.96,-0.51044,-0.85539,-0.088085,190.33
> hide #!1 models
> hide #3 models
> hide #5 models
> hide #8 models
> open /Users/mortonaj/Downloads/cryosparc_P5_J150_002_volume_map.mrc
Opened cryosparc_P5_J150_002_volume_map.mrc as #9, grid size 256,256,256,
pixel 0.83, shown at level 0.0257, step 1, values float32
> ui mousemode right zoom
> ui mousemode right translate
> show #7 models
> hide #7 models
> show #4 models
> volume #9 style mesh
> volume #9 level 0.0217
> hide #4 models
> show #2 models
> hide #2 models
> show #4 models
> hide #4 models
> show #5 models
> select add #5
4734 atoms, 4468 bonds, 665 residues, 2 models selected
> select subtract #3
942 atoms, 933 bonds, 134 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.61866,0.21509,-0.75564,117.23,0.74851,-0.4536,0.48371,108.66,-0.23872,-0.86486,-0.44162,152.21
> view matrix models
> #5,0.61866,0.21509,-0.75564,102.06,0.74851,-0.4536,0.48371,116.45,-0.23872,-0.86486,-0.44162,143.72
> fitmap #5 inMap #9
Fit molecule 5c6r.pdb1.gz (#5) to map cryosparc_P5_J150_002_volume_map.mrc
(#9) using 942 atoms
average map value = 0.0875, steps = 276
shifted from previous position = 11.8
rotated from previous position = 89.2 degrees
atoms outside contour = 14, contour level = 0.021704
Position of 5c6r.pdb1.gz (#5) relative to cryosparc_P5_J150_002_volume_map.mrc
(#9) coordinates:
Matrix rotation and translation
0.88020144 0.26965669 0.39055177 102.34651556
-0.43569009 0.13278776 0.89024802 106.79783467
0.18820084 -0.95375714 0.23436673 138.62539513
Axis -0.92913611 0.10195826 -0.35540202
Axis point 0.00000000 114.58202042 -23.63335250
Rotation angle (degrees) 82.89558340
Shift along axis -133.47266796
> view matrix models
> #5,0.8802,0.26966,0.39055,102.75,-0.43569,0.13279,0.89025,94.34,0.1882,-0.95376,0.23437,151.76
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.55862,-0.69615,0.4509,112.78,-0.69292,0.69048,0.20759,84.833,-0.45586,-0.19647,-0.8681,137.84
> view matrix models
> #5,-0.51981,0.046916,0.85299,100.23,-0.11351,0.98584,-0.1234,82.673,-0.8467,-0.16097,-0.50713,135.27
> view matrix models
> #5,-0.12596,-0.88745,0.44335,117.7,-0.43955,0.45057,0.77703,89.201,-0.88934,-0.097004,-0.44684,133.98
> view matrix models
> #5,0.72831,0.57568,0.37171,97.096,-0.6757,0.51304,0.52936,87.481,0.11404,-0.6367,0.76263,145.64
> view matrix models
> #5,-0.64114,-0.75921,0.11197,113.85,-0.75743,0.64949,0.066786,85.402,-0.12343,-0.041994,-0.99146,136.78
> view matrix models
> #5,0.19754,-0.61043,0.76704,114.09,-0.73005,0.43058,0.53068,88.62,-0.65421,-0.66482,-0.36059,144.22
> view matrix models
> #5,0.7488,-0.54725,0.37392,115.72,-0.64712,-0.72563,0.23388,108.37,0.14334,-0.4171,-0.89749,143.95
> view matrix models
> #5,-0.03395,-0.032312,-0.9989,105.54,-0.45448,0.89066,-0.013364,82.739,0.89011,0.45352,-0.044923,131.68
> view matrix models
> #5,-0.65575,-0.70554,0.26873,112.74,-0.44074,0.64673,0.62248,86.127,-0.61298,0.28975,-0.73505,129.03
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.65575,-0.70554,0.26873,115.34,-0.44074,0.64673,0.62248,88.577,-0.61298,0.28975,-0.73505,118.86
> volume #9 level 0.005883
> volume #9 level 0.01811
> volume #9 step 2
> volume #9 level 0.01847
> volume #9 step 1
> volume #9 style image
> volume #9 showOutlineBox true imageMode "tilted slab" tiltedSlabAxis
> 0.8437,0.04106,0.5352 tiltedSlabOffset 129.1 tiltedSlabSpacing 0.83
> tiltedSlabPlaneCount 51
> volume #9 maximumIntensityProjection true imageMode "full region"
> volume #9 maximumIntensityProjection false imageMode "tilted slab"
> volume #9 colorMode opaque8 imageMode "box faces"
> volume #9
> volume #9 style surface
> volume #9 style image colorMode auto8 imageMode "tilted slab"
> volume #9
> volume #9 maximumIntensityProjection true imageMode "full region"
> volume #9
> volume #9 maximumIntensityProjection false
> volume #9 colorMode opaque8 orthoplanes xyz positionPlanes 127,127,127
> imageMode orthoplanes
> volume #9
> volume #9 imageMode "box faces"
> volume #9 style surface
> volume #9 change image level -0.001168,0 level 0.02565,0.8 level 0.1388,1
> volume #9 level 0.02638
> volume #9 style mesh
> fitmap #5 inMap #9
Fit molecule 5c6r.pdb1.gz (#5) to map cryosparc_P5_J150_002_volume_map.mrc
(#9) using 942 atoms
average map value = 0.08793, steps = 168
shifted from previous position = 10.3
rotated from previous position = 48.8 degrees
atoms outside contour = 6, contour level = 0.026376
Position of 5c6r.pdb1.gz (#5) relative to cryosparc_P5_J150_002_volume_map.mrc
(#9) coordinates:
Matrix rotation and translation
-0.41359757 -0.28927268 0.86328348 106.53114494
-0.40061241 0.90928338 0.11275384 89.23863100
-0.81758593 -0.29920736 -0.49196362 121.51165947
Axis -0.23755190 0.96925081 -0.06420256
Axis point 101.50463098 0.00000000 28.11761361
Rotation angle (degrees) 119.87694720
Shift along axis 53.38657940
> ui mousemode right translate
> ui mousemode right zoom
> volume #9 level 0.05442
> volume #9 level 0.0235
> hide #!9 models
> hide #5 models
> open /Users/mortonaj/Downloads/cryosparc_P5_J150_003_volume_map_sharp.mrc
Opened cryosparc_P5_J150_003_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 0.83, shown at level 0.036, step 1, values float32
> volume #10 level 0.04719
> show #5 models
> volume #10 style mesh
> volume #10 level 0.0891
> volume #10 style surface
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.4136,-0.28927,0.86328,76.019,-0.40061,0.90928,0.11275,129.13,-0.81759,-0.29921,-0.49196,122.45
> volume #10 level 0.07787
> view matrix models
> #5,-0.4136,-0.28927,0.86328,100.53,-0.40061,0.90928,0.11275,84.367,-0.81759,-0.29921,-0.49196,116.66
> view matrix models
> #5,-0.4136,-0.28927,0.86328,100.68,-0.40061,0.90928,0.11275,91.159,-0.81759,-0.29921,-0.49196,118.15
> fitmap #5 inMap #10
Fit molecule 5c6r.pdb1.gz (#5) to map
cryosparc_P5_J150_003_volume_map_sharp.mrc (#10) using 942 atoms
average map value = 0.09186, steps = 100
shifted from previous position = 6.31
rotated from previous position = 9.91 degrees
atoms outside contour = 284, contour level = 0.077873
Position of 5c6r.pdb1.gz (#5) relative to
cryosparc_P5_J150_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.55852847 -0.24048910 0.79385826 104.73539457
-0.32383221 0.94432067 0.05823372 89.82029129
-0.76366134 -0.22455168 -0.60530810 119.37014976
Axis -0.17839377 0.98255349 -0.05257658
Axis point 91.26403376 0.00000000 33.01737923
Rotation angle (degrees) 127.57200317
Shift along axis 63.29302444
> volume #10 style mesh
> volume #10 style surface
> volume #10 color #b2b2ff74
> volume #10 level 0.116
> volume #10 level 0.1018
> zflip #10
Unknown command: zflip #10
> volume flip #10
Opened cryosparc_P5_J150_003_volume_map_sharp.mrc z flip as #11, grid size
256,256,256, pixel 0.83, shown at step 1, values float32
> view matrix models
> #5,-0.55853,-0.24049,0.79386,113.67,-0.32383,0.94432,0.058234,88.57,-0.76366,-0.22455,-0.60531,93.672
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.47027,0.74784,0.4686,101.89,-0.66996,0.64814,-0.36203,92.514,-0.57446,-0.1437,0.80582,91.562
> view matrix models
> #5,-0.43248,-0.89393,-0.11767,125.97,-0.86392,0.37349,0.33784,95.495,-0.25806,0.24777,-0.93382,88.287
> view matrix models
> #5,0.60999,0.11781,0.78361,112.51,-0.74885,0.40905,0.52144,95.174,-0.25911,-0.90488,0.33773,105.92
> view matrix models
> #5,0.75573,0.18079,0.62944,112.23,-0.32366,0.93866,0.11899,88.598,-0.56932,-0.29364,0.76789,94.1
> ui mousemode right "move picked models"
> view matrix models #11,1,0,0,4.053,0,1,0,0.27167,0,0,1,3.2865
> fitmap #5 inMap #10
Fit molecule 5c6r.pdb1.gz (#5) to map
cryosparc_P5_J150_003_volume_map_sharp.mrc (#10) using 942 atoms
average map value = 0.07132, steps = 188
shifted from previous position = 20.4
rotated from previous position = 30.8 degrees
atoms outside contour = 702, contour level = 0.10182
Position of 5c6r.pdb1.gz (#5) relative to
cryosparc_P5_J150_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.72078582 0.58265302 0.37547736 91.74296761
-0.50551514 0.81248728 -0.29037710 86.05172732
-0.47425968 0.01949020 0.88016924 72.26213242
Axis 0.21898991 0.60052751 -0.76903194
Axis point 175.87254399 -67.09009372 0.00000000
Rotation angle (degrees) 45.03123702
Shift along axis 16.19532620
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.72079,0.58265,0.37548,107.11,-0.50552,0.81249,-0.29038,86.01,-0.47426,0.01949,0.88017,87.529
> view matrix models
> #5,0.72079,0.58265,0.37548,102.43,-0.50552,0.81249,-0.29038,90.901,-0.47426,0.01949,0.88017,94.537
> fitmap #5 inMap #10
Fit molecule 5c6r.pdb1.gz (#5) to map
cryosparc_P5_J150_003_volume_map_sharp.mrc (#10) using 942 atoms
average map value = 0.08453, steps = 268
shifted from previous position = 19.3
rotated from previous position = 73.9 degrees
atoms outside contour = 668, contour level = 0.10182
Position of 5c6r.pdb1.gz (#5) relative to
cryosparc_P5_J150_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99146054 -0.01393561 0.12966028 108.54207497
0.12693353 0.33107894 -0.93502653 106.95922556
-0.02989762 0.94350015 0.33002060 95.25217650
Axis 0.99364225 0.08439778 0.07451240
Axis point 0.00000000 -11.85804501 111.68450338
Rotation angle (degrees) 70.95685626
Shift along axis 123.97658029
> view matrix models
> #5,0.99146,-0.013936,0.12966,101.06,0.12693,0.33108,-0.93503,100.23,-0.029898,0.9435,0.33002,89.755
> view matrix models
> #5,0.99146,-0.013936,0.12966,108.02,0.12693,0.33108,-0.93503,99.549,-0.029898,0.9435,0.33002,79.78
> view matrix models
> #5,0.99146,-0.013936,0.12966,113.03,0.12693,0.33108,-0.93503,97.732,-0.029898,0.9435,0.33002,76.185
> volume #10 level 0.08012
> hide #!10 models
> view matrix models
> #5,0.99146,-0.013936,0.12966,115.14,0.12693,0.33108,-0.93503,106.06,-0.029898,0.9435,0.33002,77.915
> volume #11 level 0.07114
> fitmap #5 inMap #11
Fit molecule 5c6r.pdb1.gz (#5) to map
cryosparc_P5_J150_003_volume_map_sharp.mrc z flip (#11) using 942 atoms
average map value = 0.0926, steps = 196
shifted from previous position = 3.02
rotated from previous position = 53.7 degrees
atoms outside contour = 183, contour level = 0.071137
Position of 5c6r.pdb1.gz (#5) relative to
cryosparc_P5_J150_003_volume_map_sharp.mrc z flip (#11) coordinates:
Matrix rotation and translation
0.81433658 0.35205405 0.46142590 99.74727177
-0.09980679 0.86812335 -0.48621029 93.59921019
-0.57174691 0.34988539 0.74208199 83.68325224
Axis 0.59559069 0.73597809 -0.32188194
Axis point 204.75923419 0.00000000 -2.95229831
Rotation angle (degrees) 44.58001112
Shift along axis 101.35938603
> volume #11 level 0.1152
> ui mousemode right zoom
> volume #11 level 0.08179
> volume #11 level 0.1137
> volume #11 level 0.08179
> ui mousemode right "rotate slab"
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15G001WGLL/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.2 (23B92)
Kernel Version: Darwin 23.1.0
Time since boot: 7 days, 2 hours, 17 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 23 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 23 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi AJ,
--Eric