![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16608 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 350000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 1365,
"osVersion" : {
"train" : "macOS 15.1.1",
"build" : "24B91",
"releaseType" : "User"
},
"captureTime" : "2025-01-13 15:58:47.0048 +0100",
"codeSigningMonitor" : 1,
"incident" : "5EFFDE91-9C3F-4610-A39B-540454332523",
"pid" : 17648,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-12 14:00:25.3103 +0100",
"procStartAbsTime" : 6445661865763,
"procExitAbsTime" : 8409593038661,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"4A397653-8981-5ACE-838E-6651757524B1","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C3C0CD27-A763-D1F0-B220-FD8CEDC4387B",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "F5269B7C-A6B7-4DAC-A2BC-AF57D3486FFE",
"wakeTime" : 27753,
"sleepWakeUUID" : "1A8A40BD-635D-4B5E-BB37-DCAECE58F8EB",
"sip" : "enabled",
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"os_fault" : {"process":"ChimeraX"},
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
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"arch" : "x86_64",
"base" : 6226042880,
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 6218502144,
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"uuid" : "3b76dfeb-802d-3ce8-9151-7ec4ff5a682b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6220062720,
"size" : 524288,
"uuid" : "58e1300b-c472-3863-8fc4-4eb27185cbbf",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6320963584,
"size" : 442368,
"uuid" : "9141612b-bf67-390f-8b66-18a585729cab",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 6103740416,
"size" : 32768,
"uuid" : "4cafbf15-47c9-3e93-abf0-7f8f01ea6b1d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6031933440,
"size" : 16384,
"uuid" : "ce412e76-387f-357d-b7be-b4654bc453d4",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/dssp\/_dssp.cpython-311-darwin.so",
"name" : "_dssp.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6117695488,
"size" : 16384,
"uuid" : "67c108ea-3b9a-3731-a794-8ca4049035a3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-311-darwin.so",
"name" : "_sw.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6123487232,
"size" : 16384,
"uuid" : "0cf88116-cc85-32ed-b523-593e852fc25f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/libalign_algs.dylib",
"name" : "libalign_algs.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6229938176,
"size" : 32768,
"uuid" : "ad017f10-16c5-3c7b-8ee2-47e1604a376a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-311-darwin.so",
"name" : "_nw.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6324305920,
"size" : 32768,
"uuid" : "cc4a7194-2678-3514-acc4-75a7275bf407",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
"name" : "_psutil_osx.abi3.so"
},
{
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"arch" : "x86_64",
"base" : 6148587520,
"size" : 16384,
"uuid" : "62001a43-deed-3f40-8d2d-57ad475e6c95",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
"name" : "_psutil_posix.abi3.so"
},
{
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"arch" : "x86_64",
"base" : 140703225372672,
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"size" : 21753843,
"uuid" : "3c47b8d3-238a-3e71-826e-fae5644100a7",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.20.21"
},
{
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"arch" : "x86_64",
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"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4976630,
"uuid" : "8609cb34-bab0-3736-a774-fdf7fbe44b8f",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
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"size" : 294906,
"uuid" : "b9d99f1b-62d1-357d-89a8-5ab5871d9e33",
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"logWritingSignature" : "66193842042a1230cecee9471ff0aac45453f0c4",
"trialInfo" : {
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"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x144724944)"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-62.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-62.pdb
---
warnings | Start residue of secondary structure not found: HELIX 193 193 PRO I 1336 ALA I 1343 1 8
Start residue of secondary structure not found: HELIX 194 194 ASP I 1344 ALA I
1346 1 3
Start residue of secondary structure not found: HELIX 195 195 MET I 1354 LEU I
1363 1 10
Start residue of secondary structure not found: HELIX 196 196 LEU I 1366 ALA I
1371 1 6
Start residue of secondary structure not found: HELIX 197 197 GLU I 1376 LYS I
1385 1 10
17 messages similar to the above omitted
Chain information for JF1086_model2-coot-62.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide atoms
> show cartoons
> dssp
> open
> /Users/farnung/Downloads/fold_2024_05_09_01_21(2)/fold_2024_05_09_01_21_model_0.cif
Chain information for fold_2024_05_09_01_21_model_0.cif #2
---
Chain | Description
A B | .
C | .
D | .
E | .
> mmaker #2/A to #1/A
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 JF1086_model2-coot-62.pdb, chain A (#1) with
fold_2024_05_09_01_21_model_0.cif, chain A (#2), sequence alignment score =
4069.2
RMSD between 304 pruned atom pairs is 1.153 angstroms; (across all 1016 pairs:
9.324)
> hide atoms
> show cartoons
> hide #2 models
> open /Users/farnung/Desktop/JF1086/Krios/Refined_fromJ92/composite_map.ccp4
Opened composite_map.ccp4 as #3, grid size 616,616,616, pixel 0.851, shown at
level -0.0032, step 4, values float32
> volume #3 step 1
> volume #3 level -0.003198
> volume #3 level 3.856
> combine #2
> hide #4 models
> delete #4/B-X
> delete #4/A:1-1200
> mmaker #4/A:1200-1900 #1/A:1200-1900
> matchmaker #4/A:1200-1900 #1/A:1200-1900
Missing required "to" argument
> mmaker #4/A:1200-1900 to #1/A:1200-1900
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 JF1086_model2-coot-62.pdb, chain A (#1) with copy of
fold_2024_05_09_01_21_model_0.cif, chain A (#4), sequence alignment score =
1293.6
RMSD between 156 pruned atom pairs is 1.102 angstroms; (across all 331 pairs:
4.593)
> show #4 models
> hide #!3 models
> hide #!1 models
> delete #4/A:1430-1657
> show #!1 models
> delete #4/A:100-1300
> combine #4
> mmaker #5/A to #5/H:1300-1900
No 'to' model specified
> mmaker #5/A to #1/H:1300-1900
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 JF1086_model2-coot-62.pdb, chain H (#1) with copy of copy of
fold_2024_05_09_01_21_model_0.cif, chain A (#5), sequence alignment score =
1097.9
RMSD between 116 pruned atom pairs is 0.802 angstroms; (across all 285 pairs:
5.216)
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> delete #5/A:1000-1480
> mmaker #5/A:1655-1900 to #1/H:1655-1900
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 JF1086_model2-coot-62.pdb, chain H (#1) with copy of copy of
fold_2024_05_09_01_21_model_0.cif, chain A (#5), sequence alignment score =
771.2
RMSD between 80 pruned atom pairs is 0.687 angstroms; (across all 159 pairs:
3.797)
> undo
> hide #!5 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> delete #4/A:1-1408, 1450-1900
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> combine #2
> hide #6 models
> delete #6/B-X
> delete #6/A:1-1200, 1430-1660
> show #!6 models
> mmaker #6/A:1200-1900 to #1/A:1200-1900
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 JF1086_model2-coot-62.pdb, chain A (#1) with copy of
fold_2024_05_09_01_21_model_0.cif, chain A (#6), sequence alignment score =
1285.2
RMSD between 156 pruned atom pairs is 1.102 angstroms; (across all 326 pairs:
4.573)
> combine #6
> hide #!7 models
> delete #6/A:1-1387,1430-1900
> delete #1/A:1388-1429
> show #!5 models
> hide #!5 models
> combine #1,6
Remapping chain ID 'A' in copy of fold_2024_05_09_01_21_model_0.cif #6 to 'I'
> hide #!1 models
> hide #!6 models
> save /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-62_newC-term.pdb
> models #8
> show #!3 models
> ui tool show "Fit in Map"
> hide #!3 models
> show #!3 models
> hide #!8 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!8 models
> show #!3 models
> fitmap #6 inMap #3
Fit molecule copy of fold_2024_05_09_01_21_model_0.cif (#6) to map
composite_map.ccp4 (#3) using 332 atoms
average map value = 8.215, steps = 104
shifted from previous position = 0.988
rotated from previous position = 3.16 degrees
atoms outside contour = 145, contour level = 3.8563
Position of copy of fold_2024_05_09_01_21_model_0.cif (#6) relative to
composite_map.ccp4 (#3) coordinates:
Matrix rotation and translation
-0.12613499 0.15760077 -0.97941409 255.44967363
0.90779391 0.41643741 -0.04990098 209.06491895
0.40000024 -0.89540040 -0.19559634 227.14447058
Axis -0.47409952 -0.77348328 0.42065813
Axis point -57.73663339 0.00000000 236.55561528
Rotation angle (degrees) 116.91363758
Shift along axis -187.26661865
> hide #!3 models
> show #!3 models
> hide #!3 models
> open
> /Users/farnung/Downloads/fold_armc5_cul3_dimer/fold_armc5_cul3_dimer_model_0.cif
Chain information for fold_armc5_cul3_dimer_model_0.cif #9
---
Chain | Description
A B | .
C D | .
> hide #!8 models
> color #9 bychain
> delete #9/A-C
> show #!8 models
> mmaker #9/D:1-189 to #8/F:1-189
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 combination, chain F (#8) with fold_armc5_cul3_dimer_model_0.cif,
chain D (#9), sequence alignment score = 758.2
RMSD between 121 pruned atom pairs is 1.135 angstroms; (across all 174 pairs:
3.884)
> show #!3 models
> hide #!3 models
> combine #9
> hide #10 models
> delete #9/1-26,190-1000
> delete #9/D:1-26,190-1000
> combine #9
> mmaker #9/D to #8/G:26-189
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 combination, chain G (#8) with fold_armc5_cul3_dimer_model_0.cif,
chain D (#9), sequence alignment score = 668.5
RMSD between 114 pruned atom pairs is 1.169 angstroms; (across all 163 pairs:
2.813)
> hide #9 models
> hide #11 models
> delete #8/F,G:27-500
> show #9 models
> show #11 models
> combine #8,9,11
Remapping chain ID 'D' in fold_armc5_cul3_dimer_model_0.cif #9 to 'M'
Remapping chain ID 'D' in copy of fold_armc5_cul3_dimer_model_0.cif #11 to 'N'
> hide #!8 models
> hide #9 models
> hide #11 models
> dssp
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-64.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-64.pdb
---
warnings | Start residue of secondary structure not found: HELIX 211 211 ASN I 1389 GLU I 1401 1 13
Start residue of secondary structure not found: HELIX 212 212 ALA I 1402 GLY I
1405 1 4
Start residue of secondary structure not found: HELIX 213 213 PRO I 1410 ALA I
1428 1 19
Chain information for JF1086_model2-coot-64.pdb #13
---
Chain | Description
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!12 models
> show #9 models
> show #!12 models
> hide #9#!12-13 atoms
> show #9#!12-13 cartoons
> hide #!12 models
> dssp
> delete #13/F,G:27-500
> show #11 models
> combine #13,9,11
Remapping chain ID 'D' in fold_armc5_cul3_dimer_model_0.cif #9 to 'I'
Remapping chain ID 'D' in copy of fold_armc5_cul3_dimer_model_0.cif #11 to 'M'
> hide #9 models
> hide #11 models
> hide #!13 models
> save /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-64_updated.pdb
> models #14
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-65.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-65.pdb
---
warnings | Start residue of secondary structure not found: HELIX 187 187 LYS I 28 GLN I 45 1 18
Start residue of secondary structure not found: HELIX 188 188 PHE I 54 LEU I
66 1 13
Start residue of secondary structure not found: HELIX 189 189 GLY I 70 LYS I
88 1 19
Start residue of secondary structure not found: HELIX 190 190 VAL I 89 VAL I
93 1 5
Start residue of secondary structure not found: HELIX 191 191 LEU I 94 SER I
96 1 3
19 messages similar to the above omitted
Chain information for JF1086_model2-coot-65.pdb #15
---
Chain | Description
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!14-15 atoms
> show #!14-15 cartoons
> hide #!14 models
> dssp
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-66.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-66.pdb
---
warnings | Start residue of secondary structure not found: HELIX 187 187 LYS I 28 GLN I 45 1 18
Start residue of secondary structure not found: HELIX 188 188 PHE I 54 LEU I
66 1 13
Start residue of secondary structure not found: HELIX 189 189 GLY I 70 LYS I
88 1 19
Start residue of secondary structure not found: HELIX 190 190 VAL I 89 VAL I
93 1 5
Start residue of secondary structure not found: HELIX 191 191 LEU I 94 SER I
96 1 3
19 messages similar to the above omitted
Chain information for JF1086_model2-coot-66.pdb #16
---
Chain | Description
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!15-16 atoms
> show #!15-16 cartoons
> hide #!15 models
> dssp
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-67.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-67.pdb
---
warnings | Start residue of secondary structure not found: HELIX 187 187 LYS I 28 GLN I 45 1 18
Start residue of secondary structure not found: HELIX 188 188 PHE I 54 LEU I
66 1 13
Start residue of secondary structure not found: HELIX 189 189 GLY I 70 LYS I
88 1 19
Start residue of secondary structure not found: HELIX 190 190 VAL I 89 VAL I
93 1 5
Start residue of secondary structure not found: HELIX 191 191 LEU I 94 SER I
96 1 3
19 messages similar to the above omitted
Chain information for JF1086_model2-coot-67.pdb #17
---
Chain | Description
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!16-17 atoms
> show #!16-17 cartoons
> hide #!16 models
> dssp
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-68.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-68.pdb
---
warnings | Start residue of secondary structure not found: HELIX 187 187 LYS I 28 GLN I 45 1 18
Start residue of secondary structure not found: HELIX 188 188 PHE I 54 LEU I
66 1 13
Start residue of secondary structure not found: HELIX 189 189 GLY I 70 LYS I
88 1 19
Start residue of secondary structure not found: HELIX 190 190 VAL I 89 VAL I
93 1 5
Start residue of secondary structure not found: HELIX 191 191 LEU I 94 SER I
96 1 3
19 messages similar to the above omitted
Chain information for JF1086_model2-coot-68.pdb #18
---
Chain | Description
A | No description available
B | No description available
C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!17-18 atoms
> show #!17-18 cartoons
> hide #!17 models
> dssp
> open 8q7r
8q7r title:
Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34:
NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide [more
info...]
Chain information for 8q7r #19
---
Chain | Description | UniProt
A | Cullin-2 | CUL2_HUMAN 1-745
C | Ubiquitin-conjugating enzyme E2 R2 | UB2R2_HUMAN 1-238
D | Elongin-C | ELOC_HUMAN 1-112
F | Nucleotide exchange factor SIL1 | SIL1_HUMAN 442-461
G | Elongin-B | ELOB_HUMAN 1-118
H | Protein fem-1 homolog C | FEM1C_HUMAN 1-617
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-108
U | Ubiquitin | UBC_HUMAN 1-685
Non-standard residues in 8q7r #19
---
U9O — 5-azanyl-1-oxidanyl-pentan-2-one
ZN — zinc ion
6 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!18-19 atoms
> show #!18-19 cartoons
> delete #19/A-C,F,H,R,U
> delete #19 ions
Expected a keyword
> show #19 ions
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #19 IONS
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> delete #19 ZN
Expected a keyword
> select :ZN
18 atoms, 18 residues, 9 models selected
> show sel & #!18 atoms
> hide sel & #!18 atoms
> mmaker #19/D to #18.E
> matchmaker #19/D to #18.E
Invalid "to" argument: only initial part "#18" of atom specifier valid
> mmaker #19/D to #18/E
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 JF1086_model2-coot-68.pdb, chain E (#18) with 8q7r, chain D (#19),
sequence alignment score = 441.9
RMSD between 83 pruned atom pairs is 0.676 angstroms; (across all 90 pairs:
1.433)
> select add #12
34521 atoms, 35252 bonds, 28 pseudobonds, 3644 residues, 11 models selected
> select subtract #12
16 atoms, 16 residues, 8 models selected
> select add #13
31829 atoms, 32525 bonds, 28 pseudobonds, 3316 residues, 10 models selected
> select add #14
66352 atoms, 67798 bonds, 56 pseudobonds, 6942 residues, 12 models selected
> select subtract #13
34537 atoms, 35273 bonds, 28 pseudobonds, 3640 residues, 9 models selected
> select subtract #14
12 atoms, 12 residues, 6 models selected
> select add #15
34535 atoms, 35273 bonds, 28 pseudobonds, 3638 residues, 8 models selected
> select subtract #15
10 atoms, 10 residues, 5 models selected
> select add #15
34535 atoms, 35273 bonds, 28 pseudobonds, 3638 residues, 8 models selected
> select subtract #15
10 atoms, 10 residues, 5 models selected
> select add #16
34533 atoms, 35273 bonds, 28 pseudobonds, 3636 residues, 7 models selected
> select subtract #16
8 atoms, 8 residues, 4 models selected
> select add #17
34531 atoms, 35273 bonds, 28 pseudobonds, 3634 residues, 6 models selected
> select subtract #17
6 atoms, 6 residues, 3 models selected
> select add #18
34521 atoms, 35267 bonds, 28 pseudobonds, 3632 residues, 5 models selected
> select subtract #18
4 atoms, 4 residues, 2 models selected
> combine #19
> mmaker #20/D to #18/D
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 JF1086_model2-coot-68.pdb, chain D (#18) with copy of 8q7r, chain D
(#20), sequence alignment score = 408.9
RMSD between 80 pruned atom pairs is 0.698 angstroms; (across all 90 pairs:
1.542)
> hide #!20 models
> hide #!19 models
> delete #18/B,C
> show #!19 models
> hide #!19 models
> show #!20 models
> delete #19,20/D:39-59
> delete #18/D,E:1-37,60-200
> show #!19 models
> dssp
> combine #18,19,20
Remapping chain ID 'D' in 8q7r #19 to 'I'
Remapping chain ID 'G' in 8q7r #19 to 'M'
Remapping chain ID 'D' in copy of 8q7r #20 to 'N'
Remapping chain ID 'G' in copy of 8q7r #20 to 'O'
> hide #!18 models
> hide #!19 models
> hide #!20 models
> save /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-68_updated.pdb
> models #21
> hide #!21 models
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-79.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-79.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-79.pdb #22
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!22 atoms
> show #!22 cartoons
> dssp
> open /Users/farnung/Downloads/cryosparc_P405_J92_005_volume_map.mrc
Opened cryosparc_P405_J92_005_volume_map.mrc as #23, grid size 616,616,616,
pixel 0.851, shown at level 0.00735, step 4, values float32
> volume #23 step 1
> volume #23 level 0.01687
> color /A #C400F5
> color /J #d6d71d
> color /K #0496ff
> color /L #f94144
> color /H #ba83e7
> color /G,F #20b960
> color /B,C #edafd4
> color /E,D #6266c9
> hide #!23 models
> show #!23 models
> color zone #23 near #22 distance 5.11
> color zone #23 near #22 distance 12
> hide #!23 models
> color #23 #0496ffff models
> show #!23 models
> color zone #23 near #22 distance 5.11
> color zone #23 near #22 distance 12
> hide #!23 models
> show #22/A,H:1341,1344,1345,1348,1350
> color #22/A,H:1341,1344,1345,1348,1350 red
> style #!22 stick
Changed 33268 atom styles
> open /Users/farnung/Downloads/cryosparc_P405_J180_006_volume_map.mrc
Opened cryosparc_P405_J180_006_volume_map.mrc as #24, grid size 616,616,616,
pixel 0.851, shown at level 0.00857, step 4, values float32
> volume #24 step 1
> volume #24 level 0.021
> volume #24 level 0.02431
> select add #8
31797 atoms, 32504 bonds, 28 pseudobonds, 3304 residues, 4 models selected
> select subtract #8
2 atoms, 2 residues, 1 model selected
> hide #!24 models
> select #22:K:41-47 #22/L:7-13 #22/J:600-800
2562 atoms, 2635 bonds, 269 residues, 1 model selected
> select #22:K:41-47 #22/L:7-13 #22/J:500-800
3326 atoms, 3413 bonds, 369 residues, 1 model selected
> select #22:K:41-47 #22/L:7-13 #22/J:500-900
3693 atoms, 3790 bonds, 1 pseudobond, 413 residues, 2 models selected
> molmap sel 12 onGrid #24
Opened JF1086_model2-coot-79.pdb map 12 as #25, grid size 616,616,616, pixel
0.851, shown at level 0.0338, step 1, values float32
> hide #!25 models
> select add #22
33268 atoms, 34021 bonds, 28 pseudobonds, 3627 residues, 3 models selected
> select subtract #22
Nothing selected
> select #22:K:41-47 #22/L:7-13 #22/J:500-900
3693 atoms, 3790 bonds, 1 pseudobond, 413 residues, 2 models selected
> show #!25 models
> ui mousemode right "map eraser"
> volume erase #25 center 245.92,321.99,224.59 radius 31.654
> volume erase #25 center 243.68,327.78,255.75 radius 31.654
> volume erase #25 center 281.86,298.69,313.64 radius 31.654
> volume erase #25 center 273.15,295.63,339.39 radius 31.654
> volume erase #25 center 241.66,280.86,233.74 radius 31.654
> save /Users/farnung/Desktop/JF1086/Masks/JF1086_P405_J180_mask_bulge.mrc
> models #25
> select add #22
33268 atoms, 34021 bonds, 28 pseudobonds, 3627 residues, 3 models selected
> select subtract #22
Nothing selected
> hide #!22 models
> hide #!25 models
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-80.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-80.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-80.pdb #26
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!26 atoms
> show #!26 cartoons
> ui mousemode right translate
> dssp
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-81.pdb #27
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!26-27 atoms
> show #!26-27 cartoons
> dssp
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-81.pdb #28
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!26-28 atoms
> show #!26-28 cartoons
> hide #!26 models
> hide #!27 models
> show #!27 models
> hide #!28 models
> show #!28 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> dssp
> show #!27 models
> hide #!28 models
> show #!28 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-81_updated.pdb #29
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!28-29 atoms
> show #!28-29 cartoons
> hide #!28 models
> dssp
> show #!28 models
> hide #!29 models
> show #!29 models
> hide #!28 models
> hide #!29 models
> show #!29 models
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-81_updated.pdb #29
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
---
warnings | Ignored bad PDB record found on line 336
HELIX 211 211 SER H 1320 CYS H 1329 1 10
Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I
36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-81_updated.pdb #29
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
---
warnings | Ignored bad PDB record found on line 334
HELIX 211 211 SER H 1320 CYS H 1329 1 10
Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I
36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-81_updated.pdb #29
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-81_updated.pdb #29
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-81_updated.pdb #29
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-81_updated.pdb #29
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-81_updated.pdb #29
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> dssp
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb models
> #29
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb
Chain information for JF1086_model2-coot-82.pdb #29
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb
Chain information for JF1086_model2-coot-82.pdb #29
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb
Chain information for JF1086_model2-coot-82.pdb #29
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb
Chain information for JF1086_model2-coot-82.pdb #29
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb
Chain information for JF1086_model2-coot-82.pdb #29
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-79.pdb
Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-79.pdb
---
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11
13 messages similar to the above omitted
Chain information for JF1086_model2-coot-79.pdb #29
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb
Chain information for JF1086_model2-coot-82.pdb #30
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 models
> hide #!30 cartoons
> hide #!30 atoms
> show #!30 cartoons
> delete #29
> delete #30
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb
Chain information for JF1086_model2-coot-82.pdb #29
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> delete #30
> delete #29
> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb
Chain information for JF1086_model2-coot-82.pdb #29
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
> hide #!29 atoms
> show #!29 cartoons
> hide #!29 models
> show #!23 models
> ui mousemode right "map eraser"
> volume erase #23 center 319.23,124.31,190.65 radius 58.778
Opened cryosparc_P405_J92_005_volume_map.mrc copy as #31, grid size
616,616,616, pixel 0.851, shown at step 1, values float32
> volume erase #31 center 265.85,205.46,171.57 radius 58.726
> volume erase #31 center 276.48,272.42,198.28 radius 58.726
> volume erase #31 center 227.59,338.41,226.57 radius 58.726
> volume erase #31 center 166.46,314.02,245.24 radius 58.726
> volume erase #31 center 214.68,257.02,173.13 radius 58.726
> volume erase #31 center 334.76,283.93,292.18 radius 58.726
> volume erase #31 center 282.69,311.6,324.95 radius 58.726
> volume erase #31 center 276.56,294.15,260 radius 58.726
> volume erase #31 center 259.07,260.49,212.55 radius 58.726
> volume erase #31 center 336.54,206.91,210.46 radius 58.726
> volume erase #31 center 322.07,204.83,218.59 radius 58.726
> volume #31 level 0.01947
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/farnung/Desktop/JF1086/Masks/JF1086_P405_J180_mask_3prime.mrc
> models #31
> volume erase #31 center 221.09,249.61,304.52 radius 58.726
> volume erase #31 center 261.8,248.61,340.15 radius 58.726
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save
> /Users/farnung/Desktop/JF1086/Masks/JF1086_P405_J180_mask_3prime_truncated.mrc
> models #31
> hide #!31 models
> show #!29 models
> open /Users/farnung/Downloads/cryosparc_P405_J210_003_volume_map_sharp.mrc
Opened cryosparc_P405_J210_003_volume_map_sharp.mrc as #30, grid size
616,616,616, pixel 0.851, shown at level 0.026, step 4, values float32
> ui mousemode right translate
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #30 step 1
> volume #30 level 0.06938
> volume #30 level 0.1214
> hide #!30 models
> color /A #C400F5
> color /J #d6d71d
> color /K #0496ff
> color /L #f94144
> color /H #ba83e7
> color /G,F #20b960
> color /B,C #edafd4
> color /E,D #6266c9
> color /J #fe711a
> color /J #F49E4C
> color /J #FFD166
> color /J #5BA0FC
> color /J #FFD166
> lighting soft
> graphics silhouettes true
> set bgColor white
> color /A #C400F5
> color /J #d6d71d
> color /K #0496ff
> color /L #f94144
> color /H #ba83e7
> color /G,F #20b960
> color /B,C #edafd4
> color /E,D #6266c9
> show #!3 models
> color zone #3 near #29 distance 5.11
> ui tool show "Side View"
> show #!23 models
> hide #!3 models
> volume #31 level 0.04155
> hide #!31 models
> hide #!23 models
> show #!23 models
> volume #23 level 0.02856
> volume #23 level 0.01687
> open /Users/farnung/Downloads/cryosparc_P405_J221_map.mrc
Opened cryosparc_P405_J221_map.mrc as #32, grid size 616,616,616, pixel 0.851,
shown at level 0.00592, step 4, values float32
> hide #!23 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #32 step 1
> volume #32 level 0.01543
> open /Users/farnung/Downloads/cryosparc_P405_J200_map.mrc
Opened cryosparc_P405_J200_map.mrc as #33, grid size 616,616,616, pixel 0.851,
shown at level 0.00574, step 4, values float32
> hide #!32 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #33 step 1
> volume #33 level 0.01189
> color zone #33 near #29 distance 5.11
> color zone #33 near #29 distance 12
> color zone #33 near #29 distance 14
> open /Users/farnung/Downloads/cryosparc_P405_J215_004_volume_map.mrc
Opened cryosparc_P405_J215_004_volume_map.mrc as #34, grid size 616,616,616,
pixel 0.851, shown at level 0.00901, step 4, values float32
> hide #!33 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #34 step 1
> volume #34 level 0.04074
> volume #34 level 0.02604
> open /Users/farnung/Downloads/cryosparc_P405_J219_003_volume_map.mrc
Opened cryosparc_P405_J219_003_volume_map.mrc as #35, grid size 616,616,616,
pixel 0.851, shown at level 0.00682, step 4, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #35 step 1
> volume #35 level 0.01956
> hide #!34 models
> volume #35 level 0.03039
> hide #!35 models
> show #!34 models
> show #!35 models
> hide #!34 models
> volume #35 level 0.03167
> hide #!35 models
> hide #!29 models
> show #!23 models
> ui mousemode right "map eraser"
> volume erase #23 center 270.6,282.28,324.2 radius 53.362
Opened cryosparc_P405_J92_005_volume_map.mrc copy as #37, grid size
616,616,616, pixel 0.851, shown at step 1, values float32
> volume erase #37 center 337.99,307.06,297.83 radius 53.22
> volume erase #37 center 352.14,291.25,298.12 radius 53.22
> volume erase #37 center 239.3,226.67,312.65 radius 53.22
> volume erase #37 center 253.92,167.56,285.34 radius 53.22
> volume erase #37 center 314.51,107.88,245.37 radius 53.22
> volume erase #37 center 317.08,114.39,195.11 radius 53.22
> volume erase #37 center 288.81,84.875,221.55 radius 53.22
> volume erase #37 center 179.67,328.25,256.52 radius 53.22
> volume erase #37 center 250.25,339.41,239.2 radius 53.22
> volume erase #37 center 265.23,291.28,286.65 radius 53.22
> volume erase #37 center 231.86,164.46,237.69 radius 53.22
> volume erase #37 center 240.06,295.29,272.49 radius 53.22
> ui mousemode right translate
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/farnung/Desktop/JF1086/Masks/JF1086_P405_J180_mask_5prime.mrc
> models #37
> show #!35 models
> hide #!35 models
> show #!35 models
> show #!34 models
> hide #!37 models
> hide #!34 models
> hide #!35 models
> show #!29 models
> open /Users/farnung/Downloads/cryosparc_P405_J211_map_sharp.mrc
Opened cryosparc_P405_J211_map_sharp.mrc as #36, grid size 616,616,616, pixel
0.851, shown at level 0.000367, step 4, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #36 step 1
> volume #36 level 0.0482
> ui tool show "Side View"
> volume #36 level 0.05298
> hide #!36 models
> open /Users/farnung/Downloads/cryosparc_P405_J219_006_volume_map_sharp.mrc
Opened cryosparc_P405_J219_006_volume_map_sharp.mrc as #38, grid size
616,616,616, pixel 0.851, shown at level 0.0365, step 4, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #38 step 1
> volume #38 level 0.06092
> volume #38 level 0.08809
> volume #38 level 0.08266
> hide #!38 models
> open 8tqw
Summary of feedback from opening 8tqw fetched from pdb
---
note | Fetching compressed mmCIF 8tqw from http://files.rcsb.org/download/8tqw.cif
8tqw title:
Structure of human transcriptional Mediator complex [more info...]
Chain information for 8tqw #39
---
Chain | Description | UniProt
0 | Mediator of RNA polymerase II transcription subunit 27 | MED27_HUMAN 1-311
1 | Mediator of RNA polymerase II transcription subunit 28 | MED28_HUMAN 1-178
2 | Mediator of RNA polymerase II transcription subunit 29 | MED29_HUMAN 1-200
3 | Mediator of RNA polymerase II transcription subunit 30 | MED30_HUMAN 1-178
4 | Mediator of RNA polymerase II transcription subunit 31 | MED31_HUMAN 1-131
A | Mediator of RNA polymerase II transcription subunit 1 | MED1_HUMAN 1-1581
B | Unknown Chain |
D | Mediator of RNA polymerase II transcription subunit 4 | MED4_HUMAN 1-270
F | Mediator of RNA polymerase II transcription subunit 6 | MED6_HUMAN 1-246
G | Mediator of RNA polymerase II transcription subunit 7 | MED7_HUMAN 1-233
H | Mediator of RNA polymerase II transcription subunit 8 | MED8_HUMAN 1-268
I | Mediator of RNA polymerase II transcription subunit 9 | MED9_HUMAN 1-146
J | Mediator of RNA polymerase II transcription subunit 10 | MED10_HUMAN 1-135
K | Mediator of RNA polymerase II transcription subunit 11 | MED11_HUMAN 1-117
N | Mediator of RNA polymerase II transcription subunit 14 | MED14_HUMAN 1-1454
O | Mediator of RNA polymerase II transcription subunit 15 | MED15_HUMAN 1-788
P | Mediator of RNA polymerase II transcription subunit 16 | MED16_HUMAN 1-877
Q | Mediator of RNA polymerase II transcription subunit 17 | MED17_HUMAN 1-651
R | Mediator of RNA polymerase II transcription subunit 18 | MED18_HUMAN 1-208
S | Mediator of RNA polymerase II transcription subunit 19 | MED19_HUMAN 1-244
T | Mediator of RNA polymerase II transcription subunit 20 | MED20_HUMAN 1-212
U | Mediator of RNA polymerase II transcription subunit 21 | MED21_HUMAN 1-144
V | Mediator of RNA polymerase II transcription subunit 22 | MED22_HUMAN 1-200
W | Mediator of RNA polymerase II transcription subunit 23 | MED23_HUMAN 1-1368
X | Mediator of RNA polymerase II transcription subunit 24 | MED24_HUMAN 1-989
a | Cyclin-dependent kinase 8 | CDK8_HUMAN 1-464
b | Cyclin-C | CCNC_HUMAN 1-283
c | Mediator of RNA polymerase II transcription subunit 12 | MED12_HUMAN 1-2177
d | Mediator of RNA polymerase II transcription subunit 13 | MED13_HUMAN 1-2174
Non-standard residues in 8tqw #39
---
ZN — zinc ion
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac15,3
Model Number: Z1C8000TMD/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 7 days, 2 hours, 46 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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