![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 21 months ago
Closed 21 months ago
#14484 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-14.2.1-arm64-arm-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 0x00000001e0df5000 (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" : 86000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 9112,
"osVersion" : {
"train" : "macOS 14.2.1",
"build" : "23C71",
"releaseType" : "User"
},
"captureTime" : "2024-01-26 11:59:20.2556 +0100",
"codeSigningMonitor" : 1,
"incident" : "CA833EC0-45EC-4928-A537-D2CD61528057",
"pid" : 86382,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-01-25 19:05:26.7928 +0100",
"procStartAbsTime" : 1685950305716,
"procExitAbsTime" : 2082931743358,
"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":"21F5525E-64D1-5DA1-A685-00B262EEE46C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "09AFE926-A915-5282-CACB-FD8A3A132B39",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 2,
"sleepWakeUUID" : "ECCCCC20-0034-40F7-9E97-7B85B3C4AE9F",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4338696168\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1029b4000-1029b8000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"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":86382},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4338696168\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1029b4000-1029b8000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 1-43 versus Bora 18-120 binding to
> AURKA.cxs"
Log from Sun Oct 1 16:53:59 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"
Log from Sun Oct 1 15:28:21 2023UCSF 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 1ol5
Summary of feedback from opening 1ol5 fetched from pdb
---
notes | Fetching compressed mmCIF 1ol5 from
http://files.rcsb.org/download/1ol5.cif
Fetching CCD ADP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif
1ol5 title:
Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and bound to
TPX2 1-43 [more info...]
Chain information for 1ol5 #1
---
Chain | Description | UniProt
A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403
B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN
1-43
Non-standard residues in 1ol5 #1
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
SO4 — sulfate ion
> open "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Alphafold File Bora 1-120 - Aurora A/best_model.pdb"
Chain information for best_model.pdb #2
---
Chain | Description
B | No description available
C | No description available
> MatchMaker #2 to #1
Unknown command: MatchMaker #2 to #1
> matchmaker #2 to #1 align true
Expected a keyword
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1ol5, chain A (#1) with best_model.pdb, chain B (#2), sequence
alignment score = 1379.7
RMSD between 260 pruned atom pairs is 0.622 angstroms; (across all 265 pairs:
0.926)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1ol5, chain A (#1) with best_model.pdb, chain B (#2), sequence
alignment score = 1379.7
RMSD between 260 pruned atom pairs is 0.622 angstroms; (across all 265 pairs:
0.926)
> color bychain
[Repeated 1 time(s)]
> select add #1
2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected
> select subtract #1
Nothing selected
> hide atoms
> hide #1.2 models
> show #1.2 models
> select add #1.2
1 pseudobond, 1 model selected
> select subtract #1.2
Nothing selected
> select add #1.1
13 pseudobonds, 1 model selected
> select subtract #1.1
Nothing selected
> color bychain
[Repeated 1 time(s)]
> hide #2 models
> show #2 models
> hide #2 models
> select add #1
2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected
> select subtract #1
Nothing selected
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> select #2/C:1-120
966 atoms, 992 bonds, 120 residues, 1 model selected
> color #1 #1a28ebff
> color #!1 bychain
> select add #1
3573 atoms, 3511 bonds, 14 pseudobonds, 567 residues, 4 models selected
> select subtract #1
966 atoms, 992 bonds, 120 residues, 1 model selected
> select add #2
3180 atoms, 3262 bonds, 391 residues, 1 model selected
> select subtract #2
Nothing selected
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> color #2 #28e816ff
> show #2 models
> hide #2 models
> show #2 models
> color byhetero
[Repeated 1 time(s)]
> color bychain
> show #!1 target m
> view #1 clip false
> log metadata #1
Metadata for 1ol5 #1
---
Title | Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and
bound to TPX2 1-43
Citation | Bayliss, R., Sardon, T., Vernos, I., Conti, E. (2003). Structural
Basis of Aurora-A Activation by Tpx2 at the Mitotic Spindle. Mol.Cell, 12,
851. PMID: 14580337. DOI: 10.1016/S1097-2765(03)00392-7
Non-standard residues | ADP — adenosine-5'-diphosphate
MG — magnesium ion
SO4 — sulfate ion
Gene source | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.500Å
> log chains #1
Chain information for 1ol5 #1
---
Chain | Description | UniProt
A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403
B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN
1-43
> log metadata #1
Metadata for 1ol5 #1
---
Title | Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and
bound to TPX2 1-43
Citation | Bayliss, R., Sardon, T., Vernos, I., Conti, E. (2003). Structural
Basis of Aurora-A Activation by Tpx2 at the Mitotic Spindle. Mol.Cell, 12,
851. PMID: 14580337. DOI: 10.1016/S1097-2765(03)00392-7
Non-standard residues | ADP — adenosine-5'-diphosphate
MG — magnesium ion
SO4 — sulfate ion
Gene source | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.500Å
> log chains #1
Chain information for 1ol5 #1
---
Chain | Description | UniProt
A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403
B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN
1-43
> view #1 clip false
> show #!1 target m
> show sequence
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> select #1/B:43
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:7-43
238 atoms, 244 bonds, 1 pseudobond, 30 residues, 2 models selected
> color (#!1 & sel) red
> select #2/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C
966 atoms, 992 bonds, 120 residues, 1 model selected
> color sel yellow
> select #2/B:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/B
2214 atoms, 2270 bonds, 271 residues, 1 model selected
> color sel blue
> select #1/A:377-388
90 atoms, 93 bonds, 12 residues, 1 model selected
> select #1/A:123-388
2180 atoms, 2234 bonds, 266 residues, 1 model selected
> color sel magenta
> select #2/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> save "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"
——— End of log from Sun Oct 1 15:28:21 2023 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/B:8
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:8
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:45
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:45
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/B:228-271
358 atoms, 368 bonds, 44 residues, 1 model selected
> select #2/B
2214 atoms, 2270 bonds, 271 residues, 1 model selected
> select #1/A:123-388
2180 atoms, 2234 bonds, 266 residues, 1 model selected
> select #1/B:16
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:16
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/B:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/B:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:8
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:8
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:10
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:10
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/A:123-388
2180 atoms, 2234 bonds, 266 residues, 1 model selected
> color sel blue
> select #1/B:33
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:33-35
31 atoms, 33 bonds, 3 residues, 1 model selected
> select #1/B:35
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:34-35
25 atoms, 27 bonds, 2 residues, 1 model selected
> show sel target ab
> select #2/C:103
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:103-104
22 atoms, 23 bonds, 2 residues, 1 model selected
> show sel target ab
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/C:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/C:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:15
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:15
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:25-26
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/C:25-26
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:28
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:28-30
21 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/B:13
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:13-15
21 atoms, 21 bonds, 3 residues, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:70
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:70
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/B:76
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:76
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:112
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:112
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel lime
> select #2/C:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select
> #2/B:11-13,47-53,56-68,99-106,111-131,140-142,174-176,179-182,189-205,215-223,235-244,249-251,255-260,262-267
944 atoms, 949 bonds, 113 residues, 1 model selected
> select #2/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:1-45
359 atoms, 366 bonds, 45 residues, 1 model selected
> select #2/B:1-45
359 atoms, 366 bonds, 45 residues, 1 model selected
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:41-42
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:25-26
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/C:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #1/B:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:32-35,42-45,60-66,73-85,90-105
366 atoms, 370 bonds, 44 residues, 1 model selected
> select #2/C:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> save "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"
> select #2/C:73-74
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/C:73-74
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/C:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel target a
> select #2/C:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:60-65
45 atoms, 44 bonds, 6 residues, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:62
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:62
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:66
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:66
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:59
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:59
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> save "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"
> select #2/C:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:34
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/B:34-35
25 atoms, 27 bonds, 2 residues, 1 model selected
> select #1/B:34
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/B:34
14 atoms, 15 bonds, 1 residue, 1 model selected
> save "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"
[Repeated 1 time(s)]
——— End of log from Sun Oct 1 16:53:59 2023 ———
opened ChimeraX session
> select #1/A:357-388
255 atoms, 261 bonds, 32 residues, 1 model selected
> select #1/A:123-388
2180 atoms, 2234 bonds, 266 residues, 1 model selected
> show sel surfaces
> mlp sel
Map values for surface "1ol5_A SES surface": minimum -25.48, mean 2.446e+28,
maximum 2.596e+30
To also show corresponding color key, enter the above mlp command and add key
true
> select #2/C:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1ol5 #1/A SER 388 N; 1ol5 #1/B LEU 22 N
5 hydrogen bonds found
> select #2/C:88
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:88
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:76
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:76
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:75
8 atoms, 7 bonds, 1 residue, 1 model selected
Unsupported scale factor (0.000000) detected on Display0
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.
> open "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 1-43 versus Bora 18-120 binding to
> AURKA.cxs"
Log from Sun Oct 1 16:53:59 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"
Log from Sun Oct 1 15:28:21 2023UCSF 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 1ol5
Summary of feedback from opening 1ol5 fetched from pdb
---
notes | Fetching compressed mmCIF 1ol5 from
http://files.rcsb.org/download/1ol5.cif
Fetching CCD ADP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif
1ol5 title:
Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and bound to
TPX2 1-43 [more info...]
Chain information for 1ol5 #1
---
Chain | Description | UniProt
A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403
B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN
1-43
Non-standard residues in 1ol5 #1
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
SO4 — sulfate ion
> open "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Alphafold File Bora 1-120 - Aurora A/best_model.pdb"
Chain information for best_model.pdb #2
---
Chain | Description
B | No description available
C | No description available
> MatchMaker #2 to #1
Unknown command: MatchMaker #2 to #1
> matchmaker #2 to #1 align true
Expected a keyword
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1ol5, chain A (#1) with best_model.pdb, chain B (#2), sequence
alignment score = 1379.7
RMSD between 260 pruned atom pairs is 0.622 angstroms; (across all 265 pairs:
0.926)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1ol5, chain A (#1) with best_model.pdb, chain B (#2), sequence
alignment score = 1379.7
RMSD between 260 pruned atom pairs is 0.622 angstroms; (across all 265 pairs:
0.926)
> color bychain
[Repeated 1 time(s)]
> select add #1
2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected
> select subtract #1
Nothing selected
> hide atoms
> hide #1.2 models
> show #1.2 models
> select add #1.2
1 pseudobond, 1 model selected
> select subtract #1.2
Nothing selected
> select add #1.1
13 pseudobonds, 1 model selected
> select subtract #1.1
Nothing selected
> color bychain
[Repeated 1 time(s)]
> hide #2 models
> show #2 models
> hide #2 models
> select add #1
2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected
> select subtract #1
Nothing selected
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> select #2/C:1-120
966 atoms, 992 bonds, 120 residues, 1 model selected
> color #1 #1a28ebff
> color #!1 bychain
> select add #1
3573 atoms, 3511 bonds, 14 pseudobonds, 567 residues, 4 models selected
> select subtract #1
966 atoms, 992 bonds, 120 residues, 1 model selected
> select add #2
3180 atoms, 3262 bonds, 391 residues, 1 model selected
> select subtract #2
Nothing selected
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> color #2 #28e816ff
> show #2 models
> hide #2 models
> show #2 models
> color byhetero
[Repeated 1 time(s)]
> color bychain
> show #!1 target m
> view #1 clip false
> log metadata #1
Metadata for 1ol5 #1
---
Title | Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and
bound to TPX2 1-43
Citation | Bayliss, R., Sardon, T., Vernos, I., Conti, E. (2003). Structural
Basis of Aurora-A Activation by Tpx2 at the Mitotic Spindle. Mol.Cell, 12,
851. PMID: 14580337. DOI: 10.1016/S1097-2765(03)00392-7
Non-standard residues | ADP — adenosine-5'-diphosphate
MG — magnesium ion
SO4 — sulfate ion
Gene source | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.500Å
> log chains #1
Chain information for 1ol5 #1
---
Chain | Description | UniProt
A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403
B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN
1-43
> log metadata #1
Metadata for 1ol5 #1
---
Title | Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and
bound to TPX2 1-43
Citation | Bayliss, R., Sardon, T., Vernos, I., Conti, E. (2003). Structural
Basis of Aurora-A Activation by Tpx2 at the Mitotic Spindle. Mol.Cell, 12,
851. PMID: 14580337. DOI: 10.1016/S1097-2765(03)00392-7
Non-standard residues | ADP — adenosine-5'-diphosphate
MG — magnesium ion
SO4 — sulfate ion
Gene source | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.500Å
> log chains #1
Chain information for 1ol5 #1
---
Chain | Description | UniProt
A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403
B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN
1-43
> view #1 clip false
> show #!1 target m
> show sequence
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> select #1/B:43
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:7-43
238 atoms, 244 bonds, 1 pseudobond, 30 residues, 2 models selected
> color (#!1 & sel) red
> select #2/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C
966 atoms, 992 bonds, 120 residues, 1 model selected
> color sel yellow
> select #2/B:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/B
2214 atoms, 2270 bonds, 271 residues, 1 model selected
> color sel blue
> select #1/A:377-388
90 atoms, 93 bonds, 12 residues, 1 model selected
> select #1/A:123-388
2180 atoms, 2234 bonds, 266 residues, 1 model selected
> color sel magenta
> select #2/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> save "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"
——— End of log from Sun Oct 1 15:28:21 2023 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/B:8
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:8
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:45
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:45
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/B:228-271
358 atoms, 368 bonds, 44 residues, 1 model selected
> select #2/B
2214 atoms, 2270 bonds, 271 residues, 1 model selected
> select #1/A:123-388
2180 atoms, 2234 bonds, 266 residues, 1 model selected
> select #1/B:16
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:16
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/B:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/B:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:8
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:8
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:10
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:10
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/A:123-388
2180 atoms, 2234 bonds, 266 residues, 1 model selected
> color sel blue
> select #1/B:33
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:33-35
31 atoms, 33 bonds, 3 residues, 1 model selected
> select #1/B:35
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:34-35
25 atoms, 27 bonds, 2 residues, 1 model selected
> show sel target ab
> select #2/C:103
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:103-104
22 atoms, 23 bonds, 2 residues, 1 model selected
> show sel target ab
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/C:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/C:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:15
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:15
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:25-26
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/C:25-26
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:28
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:28-30
21 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/B:13
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:13-15
21 atoms, 21 bonds, 3 residues, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:70
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:70
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/B:76
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:76
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:112
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:112
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel lime
> select #2/C:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select
> #2/B:11-13,47-53,56-68,99-106,111-131,140-142,174-176,179-182,189-205,215-223,235-244,249-251,255-260,262-267
944 atoms, 949 bonds, 113 residues, 1 model selected
> select #2/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:1-45
359 atoms, 366 bonds, 45 residues, 1 model selected
> select #2/B:1-45
359 atoms, 366 bonds, 45 residues, 1 model selected
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:41-42
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:25-26
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/C:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #1/B:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:32-35,42-45,60-66,73-85,90-105
366 atoms, 370 bonds, 44 residues, 1 model selected
> select #2/C:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> save "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"
> select #2/C:73-74
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/C:73-74
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/C:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel target a
> select #2/C:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:60-65
45 atoms, 44 bonds, 6 residues, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:56
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/C:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/C:62
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:62
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #2/C:66
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:66
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:59
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:59
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> save "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"
> select #2/C:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/C:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:34
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/B:34-35
25 atoms, 27 bonds, 2 residues, 1 model selected
> select #1/B:34
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/B:34
14 atoms, 15 bonds, 1 residue, 1 model selected
> save "/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2-
> Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"
[Repeated 1 time(s)]
——— End of log from Sun Oct 1 16:53:59 2023 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
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 Air
Model Identifier: Mac14,2
Model Number: Z160000YLFN/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 2 jours, 18 heures et 57 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PL2792H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Mirror: On
Mirror Status: Hardware Mirror
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: 2022.2.22
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 , 21 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 , 21 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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