![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15528 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff852d78640 (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
{"app_name":"ChimeraX","timestamp":"2024-06-29 21:02:30.00 +0100","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.2 (22D49)","roots_installed":0,"name":"ChimeraX","incident_id":"C05356F6-7471-4D46-8CDB-1E719EFFA37A"}
{
"uptime" : 810000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 586,
"osVersion" : {
"train" : "macOS 13.2",
"build" : "22D49",
"releaseType" : "User"
},
"captureTime" : "2024-06-29 21:02:24.9630 +0100",
"incident" : "C05356F6-7471-4D46-8CDB-1E719EFFA37A",
"pid" : 21079,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-06-29 13:20:54.3557 +0100",
"procStartAbsTime" : 782888837005569,
"procExitAbsTime" : 810579250535441,
"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":"065D341E-D3CB-5FF5-811D-052F716B724B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1952DEA2-FD81-F5D9-F84D-F6973A91273C",
"throttleTimeout" : 2147483647,
"wakeTime" : 33200,
"bridgeVersion" : {"build":"20P3045","train":"7.2"},
"sleepWakeUUID" : "31352A4C-5FC8-4B10-8F2B-DA382A13558E",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737487437800\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff20000-7ffffff21000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"ktriageinfo" : "VM - Waiting on busy page was interrupted\nVM - Fault was interrupted\nVM - Fault was interrupted\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737487437800\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff20000-7ffffff21000 [ 4K] r-x\/r-x SM=SHM ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=52.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=52.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 38.0M 10 \nCG image 1132K 94 \nColorSync 252K 29 \nCoreAnimation 1236K 112 \nCoreGraphics 8K 2 \nCoreGraphics (reserved) 8K 1 reserved VM address space (unallocated)\nCoreImage 24K 2 \nCoreServices 624K 2 \nCoreUI image data 5268K 41 \nFoundation 36K 2 \nIOKit 23.3M 3 \nImage IO 8K 1 \nKernel Alloc Once 8K 1 \nMALLOC 50.7G 2360 \nMALLOC guard page 48K 10 \nMALLOC_MEDIUM (reserved) 1.0G 12 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 132K 33 \nStack 167.3M 34 \nStack Guard 56.0M 1 \nVM_ALLOCATE 252.5M 313 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 48.2M 779 \n__DATA_CONST 53.8M 399 \n__DATA_DIRTY 1833K 230 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 214.3M 157 \n__OBJC_RO 65.5M 1 \n__OBJC_RW 1989K 2 \n__TEXT 940.7M 779 \ndyld private memory 288K 3 \nmapped file 584.8M 111 \nshared memory 3536K 34 \n=========== ======= ======= \nTOTAL 54.5G 5573 \nTOTAL, minus reserved VM space 53.1G 5573 \n",
"legacyInfo" : {
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"queue" : "com.apple.main-thread"
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"trialInfo" : {
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{
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"factorPackIds" : {
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}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ibrahim/Desktop/structures_krios_dataset/AAT9C5/AAT9C5_EMfit_intoXtalstructure.cxs
> format session
Opened postprocess.mrc as #2, grid size 180,180,180, pixel 0.93, shown at
level 0.0209, step 1, values float32
opened ChimeraX session
> close #2
> sel: 357, 358
Unknown command: sel: 357, 358
> sel/A: 357, 358
Unknown command: sel/A: 357, 358
> sel/A:357, 358
Unknown command: sel/A:357, 358
> sel/A:357-358
Unknown command: sel/A:357-358
> select /A:357-358
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:358-359
Nothing selected
> ui mousemode right select
> select /D:71
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:52
8 atoms, 7 bonds, 1 residue, 1 model selected
No visible atoms or bonds selected
> hide cartoons
> show cartoons
> hide atoms
Drag select of 20 residues
> select clear
> select /A:358-359
Nothing selected
> delete pseudobonds sel
> lighting flat
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> select /D
1611 atoms, 1655 bonds, 213 residues, 1 model selected
> color sel cornflower blue
> view sel
> view
> view sel
> view orient
> ui tool show "Side View"
> view sel
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting soft
> lighting flat
> lighting full
> lighting soft
> color sel #4f8f00ff
> select /l
1665 atoms, 1703 bonds, 215 residues, 1 model selected
> color sel #0433ffff
> color sel #9437ffff
> color sel #ff40ffff
> color sel #531b93ff
> color sel #011993ff
> color sel #005493ff
> color sel #531b93ff
> color sel #005493ff
> color sel #009193ff
> color sel #011993ff
> color sel #531b93ff
> color sel #942193ff
> color sel #941751ff
> color sel #ff2f92ff
> color sel #ff40ffff
> color sel #ff2f92ff
> color sel #ff40ffff
> color sel #0096ffff
> color sel #73fdffff
> color sel #00fa92ff
> color sel #00f900ff
> color sel #ff9300ff
> color sel #ff2600ff
> color sel #fffb00ff
> color sel #ff9300ff
> color sel #ff2600ff
> color sel #011993ff
> select clear
> ui mousemode right "translate selected models"
> view
> ui mousemode right zoom
> open /Users/ibrahim/Desktop/AAT_cryo-
> EM_paper/JI_processing_maps/Refine3D_Job131/run_class001.mrc
Opened run_class001.mrc as #2, grid size 180,180,180, pixel 0.93, shown at
level 0.00601, step 1, values float32
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule AAT9C5_refine_72.pdb (#1) to map run_class001.mrc (#2) using 6167
atoms
average map value = 0.006915, steps = 96
shifted from previous position = 6.57
rotated from previous position = 7.41 degrees
atoms outside contour = 2749, contour level = 0.0060056
Position of AAT9C5_refine_72.pdb (#1) relative to run_class001.mrc (#2)
coordinates:
Matrix rotation and translation
-0.51479242 -0.25527090 0.81842869 26.88692053
-0.85730132 0.14791624 -0.49310773 103.83806348
0.00481716 -0.95548812 -0.29499024 70.39288287
Axis -0.41553156 0.73117561 -0.54103211
Axis point 60.57486899 0.00000000 65.72421372
Rotation angle (degrees) 146.19472127
Shift along axis 26.66668601
> volume #2 level 0.001771
> volume #2 level 0.001174
> volume #2 style mesh
> hide #!2 models
> select /l
1665 atoms, 1703 bonds, 215 residues, 1 model selected
> color sel #009193ff
> color sel #008f00ff
> color sel #4f8f00ff
> color sel #929000ff
> color sel #011993ff
> color sel #005493ff
> color sel #011993ff
> color sel #531b93ff
> color sel #942193ff
> color sel #0433ffff
> color sel #011993ff
> color sel #0433ffff
> color sel #0096ffff
> color sel #0433ffff
> color sel #0096ffff
> color sel #005493ff
> color sel #9437ffff
> color sel #0433ffff
> color sel #7a81ffff
> color sel #76d6ffff
> color sel #00fdffff
> color sel #0096ffff
> color sel #ff2600ff
> color sel #ff9300ff
> color sel #ff2600ff
> color sel #0096ffff
> show #!2 models
> volume #2 style surface
> hide #!2 models
> select clear
> close #2
> open /Users/ibrahim/Desktop/AAT_cryo-
> EM_paper/JI_processing_maps/3p9A_job053/run_class001.mrc
Opened run_class001.mrc as #2, grid size 180,180,180, pixel 0.93, shown at
level 0.00561, step 1, values float32
> close #2
> open /Users/ibrahim/Desktop/AAT_cryo-
> EM_paper/JI_processing_maps/Refine3D_Job131/run_class001.mrc
Opened run_class001.mrc as #2, grid size 180,180,180, pixel 0.93, shown at
level 0.00601, step 1, values float32
> volume #2 level 0.001273
> volume #2 style mesh
> volume #2 style surface
> color #2 #b2b2b236 models
> close #2
> open /Users/ibrahim/Desktop/AAT_cryo-
> EM_paper/JI_processing_maps/PP_J131/postprocess_masked.mrc
Opened postprocess_masked.mrc as #2, grid size 180,180,180, pixel 0.93, shown
at level 0.0064, step 1, values float32
> volume #2 level 0.00687
> surface dust #2 size 9.3
> volume #2 level 0.006521
> color #2 #b2b2b26e models
> color #2 #b2b2b271 models
> color #2 #b2b2b273 models
> hide #!1 models
> show #!1 models
> color #2 #b2b2b2ff models
> volume #2 level 0.00687
> hide #!1 models
> volume #2 level 0.01512
> show #!1 models
> volume #2 level 0.007451
> open /Users/ibrahim/Desktop/AAT_cryo-
> EM_paper/JI_processing_maps/Refine3D_Job131/run_class001.mrc
Opened run_class001.mrc as #3, grid size 180,180,180, pixel 0.93, shown at
level 0.00601, step 1, values float32
> hide #!2 models
> color #3 darkgrey models
> surface dust #3 size 9.3
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> show #!3 models
> color #3 #a9a9a95e models
> ui tool show "Segment Map"
Segmenting run_class001.mrc, density threshold 0.006006
Showing 31 region surfaces
235 watershed regions, grouped to 31 regions
Showing run_class001.seg - 31 regions, 31 surfaces
> surface dust #3 size 9.3
> hide #!3 models
Hide dust shortcut requires a displayed map surface
> ui mousemode right select
> select #4.7
1 model selected
> select #4.3
1 model selected
> select #4.5
1 model selected
> select add #4.7
2 models selected
> select add #4.3
3 models selected
> select add #4.22
4 models selected
> select add #4.10
5 models selected
Grouped 5 regions
> select add #4.11
2 models selected
Grouped 2 regions
> select add #4.20
2 models selected
> select add #4.29
3 models selected
> select add #4.17
4 models selected
Grouped 4 regions
> color #4 #b2b2b26d
> color #4 #b2b2b26e
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> close #4
Segmenting run_class001.mrc, density threshold 0.006006
Showing 31 region surfaces
235 watershed regions, grouped to 31 regions
Showing run_class001.seg - 31 regions, 31 surfaces
> show #!2 models
> hide #!2 models
> select add #4.3
1 model selected
> select add #4.22
2 models selected
> select add #4.31
3 models selected
> select add #4.5
4 models selected
> select add #4.27
5 models selected
> select add #4.30
6 models selected
> select add #4.25
7 models selected
> select add #4.20
8 models selected
> select add #4.10
9 models selected
> select subtract #4.10
8 models selected
> select add #4.29
9 models selected
> select add #4.17
10 models selected
> select add #4.18
11 models selected
Grouped 11 regions
> select add #4.28
2 models selected
Grouped 2 regions
> select add #4.19
2 models selected
Drag select of 357, 6 of 9440 triangles, 366, 6 of 63672 triangles, 1 residues
Grouped 2 regions
> select add #4.3
5 atoms, 1 residue, 3 models selected
> select subtract #4.5
5 atoms, 1 residue, 2 models selected
Grouped 1 regions
> select add #4.7
5 atoms, 1 residue, 3 models selected
> select add #4.5
5 atoms, 1 residue, 4 models selected
> select subtract #4.5
5 atoms, 1 residue, 3 models selected
Grouped 2 regions
> select add #4.5
5 atoms, 1 residue, 3 models selected
Grouped 2 regions
> select add #4.16
5 atoms, 1 residue, 3 models selected
Segmenting run_class001.mrc, density threshold 0.006006
Showing 31 region surfaces
235 watershed regions, grouped to 31 regions
Showing run_class001.seg - 31 regions, 31 surfaces
> select add #4.16
5 atoms, 1 residue, 2 models selected
> select add #4.7
5 atoms, 1 residue, 3 models selected
Drag select of 358, 3812 of 20944 triangles, 363, 359, 8393 of 12548
triangles, 344, 10551 of 10660 triangles, 353, 362, 357, 66 of 6692 triangles,
356, 360, 329, 326, 350, 355, 196, 339, 2860 of 3764 triangles, 248, 327, 287,
153, 240, 2314 of 3220 triangles, 387 residues
Drag select of 358, 341 of 20944 triangles, 363, 14875 of 15560 triangles,
359, 3998 of 12548 triangles, 344, 7999 of 10660 triangles, 353, 362, 356,
6570 of 7208 triangles, 360, 329, 6718 of 6800 triangles, 326, 350, 355, 4977
of 5520 triangles, 196, 339, 738 of 3764 triangles, 248, 3155 of 3424
triangles, 327, 287, 153, 240, 772 of 3220 triangles, 327 residues
Grouped 19 regions
> select clear
> select add #4.15
1 model selected
> select add #4.9
2 models selected
Grouped 2 regions
> select add #4.23
2 models selected
Grouped 2 regions
> select add #4.24
2 models selected
Grouped 2 regions
> select #4.4
1 model selected
Segmenting run_class001.mrc, density threshold 0.006006
Showing 31 region surfaces
235 watershed regions, grouped to 31 regions
Showing run_class001.seg - 31 regions, 31 surfaces
> select #4.1
1 model selected
Segmenting run_class001.mrc, density threshold 0.006006
Showing 31 region surfaces
235 watershed regions, grouped to 31 regions
Showing run_class001.seg - 31 regions, 31 surfaces
Segmenting run_class001.mrc, density threshold 0.006006
Showing 12 region surfaces
235 watershed regions, grouped to 12 regions
Showing run_class001.seg - 12 regions, 12 surfaces
Segmenting run_class001.mrc, density threshold 0.006006
Showing 31 region surfaces
235 watershed regions, grouped to 31 regions
Showing run_class001.seg - 31 regions, 31 surfaces
> select add #4.5
1 model selected
> select add #4.28
2 models selected
> select add #4.18
3 models selected
> select add #4.29
4 models selected
> select add #4.17
5 models selected
> select add #4.3
6 models selected
> select add #4.19
7 models selected
> select add #4.20
8 models selected
> select add #4.10
9 models selected
> select add #4.25
10 models selected
> select add #4.30
11 models selected
> select add #4.11
12 models selected
> select add #4.16
13 models selected
Grouped 13 regions
> select add #4.7
2 models selected
> select add #4.22
3 models selected
Grouped 3 regions
> select add #4.31
2 models selected
Grouped 2 regions
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select #4.1
1 model selected
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> select subtract #4.1
Nothing selected
> select add #4.1
1 model selected
Segmenting run_class001.mrc, density threshold 0.006006
Showing 31 region surfaces
235 watershed regions, grouped to 31 regions
Showing run_class001.seg - 31 regions, 31 surfaces
> volume #2 level 0.008648
> hide #!2 models
> select #4.1
1 model selected
Ungrouped to 4 regions
Ungrouped to 11 regions
> select add #4.3
12 models selected
> select add #4.22
13 models selected
> select add #4.7
14 models selected
> select add #4.5
15 models selected
> select add #4.16
16 models selected
> select add #4.11
17 models selected
> select add #4.20
18 models selected
> select add #4.19
19 models selected
> select subtract #4.20
18 models selected
> select #4.20
1 model selected
> select add #4.25
2 models selected
> select add #4.10
3 models selected
Grouped 3 regions
> select add #4.11
2 models selected
> select add #4.30
3 models selected
Grouped 3 regions
> select add #4.16
2 models selected
> select add #4.27
3 models selected
Grouped 3 regions
> select add #4.28
2 models selected
> select add #4.5
3 models selected
Grouped 3 regions
> select add #4.18
2 models selected
> select add #4.17
3 models selected
> select add #4.29
4 models selected
> select add #4.19
5 models selected
> select add #4.3
6 models selected
Grouped 6 regions
> select add #4.22
2 models selected
> select add #4.7
3 models selected
Grouped 3 regions
> select add #4.31
2 models selected
Grouped 2 regions
> select add #4.37
2 models selected
Grouped 2 regions
> select clear
> select #4.4
1 model selected
Ungrouped to 3 regions
> select #4.15
1 model selected
> select add #4.14
2 models selected
> select clear
> select add #4.15
1 model selected
> select add #4.14
2 models selected
> select add #4.9
3 models selected
> select add #4.24
4 models selected
> select add #4.8
5 models selected
Grouped 5 regions
> select add #4.7
2 models selected
Grouped 2 regions
> select clear
> select add #4.38
1 model selected
> select clear
> select add #4.23
1 model selected
> select add #4.10
2 models selected
> select add #4.4
3 models selected
Grouped 3 regions
> select add #4.12
2 models selected
> select add #4.21
3 models selected
Grouped 3 regions
> select clear
> select add #4.38
1 model selected
> select add #4.26
2 models selected
> select add #4.42
3 models selected
> select subtract #4.26
2 models selected
> select add #4.26
3 models selected
> select add #4.43
4 models selected
> select add #4.39
5 models selected
> select add #4.41
6 models selected
> select add #4.1
7 models selected
> select add #4.36
8 models selected
> select add #4.13
9 models selected
> select add #4.2
10 models selected
> select add #4.6
11 models selected
Grouped 11 regions
> select add #4.44
2 models selected
> select add #4.45
3 models selected
Grouped 3 regions
> select add #4.5
2 models selected
Grouped 2 regions
> hide #4.40 models
> show #4.40 models
> hide #4.40 models
> show #4.40 models
> select add /L:26
6 atoms, 5 bonds, 1 residue, 2 models selected
> select clear
> select add #4.40
1 model selected
> select add #4.1
2 models selected
Grouped 2 regions
> hide #4.4 models
> show #4.4 models
> select clear
> ui mousemode right zoom
> color #4.1 darkgrey
> color #4.4 #4f8f00ff
> color #4.1 #0433ffff
> color #4.3 darkgrey
> hide #!1 models
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> ui mousemode right select
> select #4.3
1 model selected
> select #4.3
1 model selected
> select clear
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> hide #!4 models
> show #!4 models
> ui mousemode right translate
> save /Users/ibrahim/Desktop/image188.png supersample 3
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> save /Users/ibrahim/Desktop/image189.png supersample 3
> save /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/AAT_9c5_mapsegmentation.cxs includeMaps true
> hide #!4 models
> show #!1 models
> show #!2 models
> volume #3 level 0.006467
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #2 level 0.006852
> volume #2 level 0.007331
Segmenting postprocess_masked.mrc, density threshold 0.007331
Showing 35 region surfaces
475 watershed regions, grouped to 35 regions
Showing postprocess_masked.seg - 35 regions, 35 surfaces
> surface dust #2 size 9.3
> close #4
> surface dust #2 size 9.3
Segmenting postprocess_masked.mrc, density threshold 0.007331
Showing 35 region surfaces
475 watershed regions, grouped to 35 regions
Showing postprocess_masked.seg - 35 regions, 35 surfaces
> ui mousemode right select
> select add #4.12
1 model selected
> select add #4.8
2 models selected
> select add #4.13
3 models selected
> select add #4.7
4 models selected
> select add #4.5
5 models selected
Grouped 5 regions
> select add #4.22
2 models selected
> select add #4.4
3 models selected
> select add #4.30
4 models selected
> select add #4.25
5 models selected
> select add #4.19
6 models selected
> select add #4.18
7 models selected
> select add #4.33
8 models selected
> select add #4.15
9 models selected
Grouped 9 regions
> select add #4.28
2 models selected
> select add #4.27
3 models selected
> select add #4.26
4 models selected
Grouped 4 regions
> select add #4.34
2 models selected
Grouped 2 regions
> select add #4.20
2 models selected
Grouped 2 regions
> select #4.4
1 model selected
Ungrouped to 2 regions
Segmenting postprocess_masked.mrc, density threshold 0.007331
Showing 35 region surfaces
475 watershed regions, grouped to 35 regions
Showing postprocess_masked.seg - 35 regions, 35 surfaces
> select #4.25
1 model selected
Ungrouped to 2 regions
> select #4.2
1 model selected
Ungrouped to 4 regions
> select add #4.4
5 models selected
> select add #4.22
6 models selected
> select add #4.8
7 models selected
> select add #4.7
8 models selected
> select add #4.12
9 models selected
Drag select of 694, 9371 of 19360 triangles, 690, 698, 9508 of 12836
triangles, 660, 691, 10483 of 10496 triangles, 708, 707, 706, 1240 of 8652
triangles, 696, 699, 3082 of 7064 triangles, 684, 693, 702, 704, 705, 609,
594, 710, 709, 621, 3998 of 4324 triangles, 674, 584, 681, 2217 of 3268
triangles, 480, 428 residues, 2 postprocess_masked.mrc
> select clear
> select add #4.15
1 model selected
> select add #4.20
2 models selected
> select add #4.4
3 models selected
> select add #4.8
4 models selected
> select add #4.22
5 models selected
> select add #4.5
6 models selected
> select add #4.7
7 models selected
> select add #4.12
8 models selected
> select add #4.18
9 models selected
> select add #4.19
10 models selected
Grouped 10 regions
> select add #4.30
2 models selected
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!4 models
> select subtract #4.30
1 model selected
Grouped 1 regions
> select subtract #4.2
Nothing selected
> select clear
> select add #4.30
1 model selected
> select add #4.2
2 models selected
Grouped 2 regions
> select add #4.33
2 models selected
> select add #4.24
3 models selected
> select add #4.34
4 models selected
> select add #4.27
5 models selected
> select add #4.28
6 models selected
> select add #4.26
7 models selected
Grouped 7 regions
> select add #4.13
2 models selected
Grouped 2 regions
> select add #4.29
2 models selected
> select add #4.16
3 models selected
> select add #4.3
4 models selected
> select add #4.31
5 models selected
> select add #4.35
6 models selected
> select add #4.38
7 models selected
Grouped 7 regions
Ungrouped to 7 regions
> select clear
> select add #4.8
1 model selected
> select add #4.7
2 models selected
Grouped 2 regions
> select add #4.3
2 models selected
Grouped 2 regions
Grouped 1 regions
> select #4.13
1 model selected
> select add #4.2
2 models selected
Grouped 2 regions
> select add #4.1
2 models selected
> select add #4.11
3 models selected
Grouped 3 regions
> select add #4.36
2 models selected
Grouped 2 regions
> select add #4.12
2 models selected
Grouped 2 regions
> select add #4.4
2 models selected
Grouped 2 regions
> select add #4.23
2 models selected
> select clear
> select add #4.23
1 model selected
> select add #4.9
2 models selected
> select add #4.14
3 models selected
Grouped 3 regions
> select add #4.39
2 models selected
> select add #4.32
3 models selected
Grouped 3 regions
> select add #4.6
2 models selected
> select add #4.10
3 models selected
Grouped 3 regions
> select add #4.25
2 models selected
> select add #4.17
3 models selected
Grouped 3 regions
> select clear
> select add #4.37
1 model selected
> select add #4.1
2 models selected
Grouped 2 regions
> hide #4.2 models
> show #4.2 models
> hide #4.5 models
> show #4.5 models
> hide #4.21 models
> show #4.21 models
> hide #4.21 models
> show #4.21 models
> select clear
> select add #4.21
1 model selected
> select add #4.2
2 models selected
Grouped 2 regions
> color #4.5 darkgrey
> color #4.5 #929292ff
> color #4.5 darkgrey
> select subtract #4.2
Nothing selected
> select add #4.2
1 model selected
> select clear
> select add #4.2
1 model selected
> color #4.5 #005493ff
> color #4.5 darkgrey
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #4.40
2 models selected
> select subtract #4.40
1 model selected
Grouped 1 regions
> select clear
> select #4.2
1 model selected
> select add #4.40
2 models selected
> select subtract #4.40
1 model selected
Grouped 1 regions
> select subtract #4.2
Nothing selected
Smoothing and grouping, standard deviation 5 voxels
No new groups smoothing 5 voxels
No new groups smoothing 6 voxels
Showing 3 region surfaces
Got 3 regions after smoothing 7 voxels.
> select add #4.1
1 model selected
> select clear
> ui mousemode right zoom
> color #4.2 #4f8f00ff
> color #4.1 #0096ffff
> hide #!4 models
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> save /Users/ibrahim/Desktop/image189.png supersample 3
> save /Users/ibrahim/Desktop/image190.png supersample 3
> save /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/AAT_9c5_mapsegmentation.cxs includeMaps true
> hide #!4 models
> show #!3 models
> open "/Users/ibrahim/Desktop/breach_schematic 3.cxs"
opened ChimeraX session
> show #!18 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> show #!19 models
> show #!20 models
> hide #!20 models
> hide #!19 models
> show #!19 models
> show #!20 models
> hide #!20 models
> close session
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/AAT_9c5_mapsegmentation.cxs format session
Opened postprocess_masked.mrc as #2, grid size 180,180,180, pixel 0.93, shown
at level 0.00733, step 1, values float32
Opened run_class001.mrc as #3, grid size 180,180,180, pixel 0.93, shown at
level 0.00647, step 1, values float32
opened ChimeraX session
Showing postprocess_masked.seg - 3 regions, 3 surfaces
> open "/Users/ibrahim/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/FA48D6E5-A34F-48C5-88DF-27B28F822657/C-terminal.pdb"
Chain information for C-terminal.pdb #5
---
Chain | Description
A B | No description available
> hide #4.3 models
> hide #4.2 models
> hide #4.1 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!3 models
> ui mousemode right "translate selected models"
> hide #!5 models
> show #!5 models
> select add #5
5746 atoms, 5862 bonds, 4 pseudobonds, 736 residues, 2 models selected
> view matrix models #5,1,0,0,36.665,0,1,0,45.639,0,0,1,63.455
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.83063,-0.47862,-0.28455,2.0326,-0.24717,-0.14099,0.95866,54.799,-0.49895,0.86663,-0.0011884,41.199
> view matrix models
> #5,-0.83472,-0.45484,-0.31043,1.7181,-0.30262,-0.092101,0.94865,50.821,-0.46007,0.8858,-0.060764,43.932
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.83472,-0.45484,-0.31043,68.707,-0.30262,-0.092101,0.94865,69.162,-0.46007,0.8858,-0.060764,27.827
> view matrix models
> #5,-0.83472,-0.45484,-0.31043,67.781,-0.30262,-0.092101,0.94865,69.101,-0.46007,0.8858,-0.060764,27.332
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.68859,-0.71933,-0.091722,77.55,-0.22187,0.088567,0.97105,62.763,-0.69038,0.689,-0.22058,33.972
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.68859,-0.71933,-0.091722,82.12,-0.22187,0.088567,0.97105,64.683,-0.69038,0.689,-0.22058,27.905
> view matrix models
> #5,-0.68859,-0.71933,-0.091722,82.73,-0.22187,0.088567,0.97105,65.176,-0.69038,0.689,-0.22058,26.652
> ui tool show "Fit in Map"
> fitmap #5 inMap #3
Fit molecule C-terminal.pdb (#5) to map run_class001.mrc (#3) using 5746 atoms
average map value = 0.003533, steps = 480
shifted from previous position = 9.65
rotated from previous position = 45.6 degrees
atoms outside contour = 4232, contour level = 0.0064672
Position of C-terminal.pdb (#5) relative to run_class001.mrc (#3) coordinates:
Matrix rotation and translation
-0.26270287 -0.92435377 -0.27668992 114.00212984
0.21209049 -0.33506823 0.91801248 108.39442042
-0.94127830 0.18248121 0.28407003 22.99610895
Axis -0.48773937 0.44069631 0.75358946
Axis point 32.97667310 83.29454990 -0.00000000
Rotation angle (degrees) 131.06011654
Shift along axis 9.49531919
> view matrix models
> #5,-0.2627,-0.92435,-0.27669,114.74,0.21209,-0.33507,0.91801,107.92,-0.94128,0.18248,0.28407,23.718
> fitmap #5 inMap #3
Fit molecule C-terminal.pdb (#5) to map run_class001.mrc (#3) using 5746 atoms
average map value = 0.003533, steps = 100
shifted from previous position = 1.13
rotated from previous position = 0.0243 degrees
atoms outside contour = 4231, contour level = 0.0064672
Position of C-terminal.pdb (#5) relative to run_class001.mrc (#3) coordinates:
Matrix rotation and translation
-0.26308182 -0.92422207 -0.27676983 113.97633770
0.21214186 -0.33527118 0.91792651 108.40500450
-0.94116088 0.18277530 0.28426993 22.98700631
Axis -0.48759496 0.44066272 0.75370254
Axis point 32.97294477 83.28221601 0.00000000
Rotation angle (degrees) 131.07463149
Shift along axis 9.52112103
> hide #!5 models
> volume #3 level 0.001137
> show #!5 models
> hide #!5 models
> color #3 darkgrey models
> hide #!3 models
> show #!3 models
> color #3 darkgrey models
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting shadows true intensity 0.5
> color #3 #797979ff models
> view matrix models
> #5,-0.26308,-0.92422,-0.27677,116.23,0.21214,-0.33527,0.91793,79.166,-0.94116,0.18278,0.28427,22.557
> undo
> show #!5 models
> volume #3 level 0.001336
> hide #!5 models
> view matrix models
> #5,-0.26308,-0.92422,-0.27677,137.12,0.21214,-0.33527,0.91793,75.267,-0.94116,0.18278,0.28427,32.344
> undo
> copy #3
Unknown command: copy #3
> vop add #3
Opened run_class001.mrc resampled as #6, grid size 180,180,180, pixel 0.93,
shown at step 1, values float32
> select subtract #5
Nothing selected
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!6 models
> show #!6 models
> show #!5 models
> color #3 #79797980 models
> color #3 #7979793c models
> color #3 #79797931 models
> hide #!6 models
> color #3 #79797930 models
> select add #5
5746 atoms, 5862 bonds, 4 pseudobonds, 736 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.53469,-0.77374,0.33976,74.127,0.80711,-0.34847,0.4766,147.28,-0.25037,0.52905,0.81082,12.805
> view matrix models
> #5,-0.35719,0.86651,0.34866,3.229,0.1062,0.40855,-0.90654,136.81,-0.92797,-0.28678,-0.23795,64.815
> view matrix models
> #5,-0.33462,0.87684,0.34521,3.7044,0.12698,0.40495,-0.90548,137.71,-0.93376,-0.25916,-0.24684,63.63
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.33462,0.87684,0.34521,21.243,0.12698,0.40495,-0.90548,140.88,-0.93376,-0.25916,-0.24684,114.85
> hide #!3 models
> show #!3 models
> volume #3 level 0.007542
> fitmap #5 inMap #3
Fit molecule C-terminal.pdb (#5) to map run_class001.mrc (#3) using 5746 atoms
average map value = 0.003426, steps = 376
shifted from previous position = 13.9
rotated from previous position = 7.07 degrees
atoms outside contour = 4592, contour level = 0.0075421
Position of C-terminal.pdb (#5) relative to run_class001.mrc (#3) coordinates:
Matrix rotation and translation
-0.26173374 0.92519153 0.27480191 20.99180368
0.20308093 0.33114640 -0.92146634 133.48528707
-0.94353251 -0.18537180 -0.27456094 111.90406719
Axis 0.46117575 0.76330725 -0.45241459
Axis point 15.66895877 0.00000000 97.83127813
Rotation angle (degrees) 127.05448004
Shift along axis 60.94416672
> select subtract #5
Nothing selected
> show #!1 models
> hide #!5 models
> ui mousemode right zoom
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> color #3 darkgrey models
> show #!1 models
> color #3 silver models
> color #3 #929292ff models
> color #3 darkgrey models
> lighting full
> lighting soft
> volume #3 level 0.001182
> color #3 #a9a9a971 models
> color #3 #a9a9a970 models
> color #3 #a9a9a96f models
> color #3 #a9a9a96e models
> show #!6 models
> select add #6
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,64.42,0,1,0,-11.163,0,0,1,58.167
> volume #6 level 0.00118
> ui mousemode right zoom
> show #!5 models
> volume #6 level 0.001129
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,82.373,0,1,0,-103.53,0,0,1,20.655
> view matrix models #6,1,0,0,43.75,0,1,0,-28.584,0,0,1,49.013
> hide #!5 models
> view matrix models #6,1,0,0,55.633,0,1,0,-30.215,0,0,1,66.845
> view matrix models #6,1,0,0,62.029,0,1,0,-17.652,0,0,1,40.42
> view matrix models #6,1,0,0,58.703,0,1,0,-10.237,0,0,1,48.488
> view matrix models #6,1,0,0,52.498,0,1,0,-7.5398,0,0,1,46.054
> show #!5 models
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.98765,0.15635,0.0098803,39.942,-0.1554,0.98572,-0.064929,12.036,-0.019891,0.062592,0.99784,42.788
> view matrix models
> #6,0.99946,0.031652,0.008564,49.174,-0.030355,0.99189,-0.12343,7.3049,-0.012401,0.1231,0.99232,37.858
> view matrix models
> #6,0.12856,0.12252,-0.98411,205.27,0.30526,0.93927,0.15681,-41.649,0.94355,-0.32057,0.08335,85.346
> view matrix models
> #6,0.13247,0.13503,-0.98195,203.75,0.30504,0.93704,0.17,-42.715,0.94308,-0.32206,0.08294,85.542
> view matrix models
> #6,0.13501,0.1971,-0.97104,197.52,0.26222,0.93797,0.22684,-44.859,0.95552,-0.28525,0.074949,82.368
> view matrix models
> #6,0.45472,-0.12028,-0.88248,189.45,0.30416,0.95224,0.026935,-30.184,0.83709,-0.28066,0.46958,53.563
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.45472,-0.12028,-0.88248,142.37,0.30416,0.95224,0.026935,-13.454,0.83709,-0.28066,0.46958,77.625
> view matrix models
> #6,0.45472,-0.12028,-0.88248,134.76,0.30416,0.95224,0.026935,-15.421,0.83709,-0.28066,0.46958,74.962
> view matrix models
> #6,0.45472,-0.12028,-0.88248,151.86,0.30416,0.95224,0.026935,-32.622,0.83709,-0.28066,0.46958,77.477
> color #6 #b2ffff80 models
> color #6 #b2ffff61 models
> ui mousemode right zoom
> hide #!5 models
> show #!5 models
> hide #!5 models
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.45472,-0.12028,-0.88248,165.07,0.30416,0.95224,0.026935,-30.878,0.83709,-0.28066,0.46958,74.053
> view matrix models
> #6,0.45472,-0.12028,-0.88248,173.35,0.30416,0.95224,0.026935,-30.864,0.83709,-0.28066,0.46958,76.142
> view matrix models
> #6,0.45472,-0.12028,-0.88248,165.59,0.30416,0.95224,0.026935,-28.325,0.83709,-0.28066,0.46958,71.166
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.53898,0.045918,-0.84106,141.63,0.34929,0.89643,0.27278,-50.897,0.76648,-0.4408,0.46712,89.839
> view matrix models
> #6,0.7187,0.021099,-0.695,115.53,0.23517,0.93326,0.27153,-44.768,0.65434,-0.35859,0.66577,73.039
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.7187,0.021099,-0.695,127.56,0.23517,0.93326,0.27153,-50.618,0.65434,-0.35859,0.66577,71.212
> view matrix models
> #6,0.7187,0.021099,-0.695,130.76,0.23517,0.93326,0.27153,-42.389,0.65434,-0.35859,0.66577,66.868
> view matrix models
> #6,0.7187,0.021099,-0.695,128.98,0.23517,0.93326,0.27153,-41.667,0.65434,-0.35859,0.66577,68.593
> show #!5 models
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.7187,0.021099,-0.695,128.34,0.23517,0.93326,0.27153,-36.642,0.65434,-0.35859,0.66577,71.601
> hide #!5 models
> view matrix models
> #6,0.7187,0.021099,-0.695,129.29,0.23517,0.93326,0.27153,-35.692,0.65434,-0.35859,0.66577,71.13
> open "/Users/ibrahim/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/CFABD82F-90D9-49F7-93DF-45DAEE492938/C-terminal.pdb"
Chain information for C-terminal.pdb #7
---
Chain | Description
A B | No description available
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!3 models
> show #!4 models
> ui mousemode right translate
> show #!7 models
> select subtract #6
Nothing selected
> select add #7
5746 atoms, 5862 bonds, 4 pseudobonds, 736 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.09978,0.30201,0.94807,-82.428,-0.29813,0.91812,-0.2611,2.4656,-0.94929,-0.2566,0.18165,7.1774
> view matrix models
> #7,-0.18788,0.95308,0.23737,-97.456,-0.37014,0.15515,-0.91593,59.833,-0.90978,-0.25995,0.32362,3.5586
> view matrix models
> #7,-0.33639,0.8184,0.46589,-105.04,-0.63872,0.16526,-0.75148,43.37,-0.69201,-0.55037,0.46714,19.966
> view matrix models
> #7,-0.47324,0.53589,0.69919,-105.42,-0.80176,0.066832,-0.59389,36.162,-0.36499,-0.84164,0.39803,48.293
> show #!3 models
> view matrix models
> #7,-0.62202,-0.77662,-0.099719,-19.73,0.58607,-0.37733,-0.71704,112.86,0.51924,-0.50446,0.68987,54.342
> view matrix models
> #7,0.26448,0.35146,-0.89807,-10.576,0.24476,0.87627,0.41501,-0.44663,0.93281,-0.32958,0.14574,81.468
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.26448,0.35146,-0.89807,-18.476,0.24476,0.87627,0.41501,-5.0627,0.93281,-0.32958,0.14574,53.776
> hide #!7 models
> show #!5 models
> hide #!6 models
> view matrix models
> #7,0.26448,0.35146,-0.89807,-10.652,0.24476,0.87627,0.41501,-9.2421,0.93281,-0.32958,0.14574,53.511
> ui mousemode right zoom
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> select #5/A
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> hide #!5 models
> show #!7 models
> select clear
> select #7/A
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> hide #7.1 models
> show #7.1 models
> hide #7.1 models
> show #7.1 models
> select add #7.1
2 pseudobonds, 1 model selected
> select subtract #7.1
Nothing selected
> save /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot.pdb models #7
> show #!5 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!3 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v1.pdb
Chain information for C-terminal_single_subunit_before_coot-v1.pdb #8
---
Chain | Description
B | No description available
> hide #7.1 models
> select add #8
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.99708,0.026632,0.071609,-3.5127,-0.024128,0.99907,-0.035608,0.28485,-0.072491,0.033776,0.9968,-3.9929
> view matrix models
> #8,0.9236,0.15956,0.34856,-20.651,-0.094117,0.97581,-0.19732,3.8407,-0.37161,0.14944,0.91628,-17.325
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.9236,0.15956,0.34856,51.221,-0.094117,0.97581,-0.19732,-5.4643,-0.37161,0.14944,0.91628,54.502
> view matrix models
> #8,0.9236,0.15956,0.34856,86.807,-0.094117,0.97581,-0.19732,66.167,-0.37161,0.14944,0.91628,16.976
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.00467,0.83142,-0.55563,46.654,0.99254,0.063846,0.10388,141.18,0.12184,-0.55197,-0.82491,118.37
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.00467,0.83142,-0.55563,59.797,0.99254,0.063846,0.10388,137.4,0.12184,-0.55197,-0.82491,159.21
> view matrix models
> #8,0.00467,0.83142,-0.55563,59.487,0.99254,0.063846,0.10388,135.49,0.12184,-0.55197,-0.82491,160.86
> view matrix models
> #8,0.00467,0.83142,-0.55563,58.974,0.99254,0.063846,0.10388,134.42,0.12184,-0.55197,-0.82491,157.65
> view matrix models
> #8,0.00467,0.83142,-0.55563,58.258,0.99254,0.063846,0.10388,134.87,0.12184,-0.55197,-0.82491,157.36
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.12632,0.88791,-0.44233,55.817,0.97794,-0.036677,0.20565,137.11,0.16637,-0.45855,-0.87295,154.96
> view matrix models
> #8,0.18043,0.87846,-0.44244,58.006,0.97647,-0.10597,0.18782,141.33,0.11811,-0.46592,-0.87691,153.98
> ui mousemode right zoom
> ui tool show Matchmaker
> matchmaker #!8 to #5
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 C-terminal.pdb, chain A (#5) with
C-terminal_single_subunit_before_coot-v1.pdb, chain B (#8), sequence alignment
score = 1880.5
RMSD between 325 pruned atom pairs is 0.054 angstroms; (across all 368 pairs:
9.558)
> undo
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!1 models
> matchmaker #!8 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 AAT9C5_refine_72.pdb, chain A (#1) with
C-terminal_single_subunit_before_coot-v1.pdb, chain B (#8), sequence alignment
score = 1782.1
RMSD between 328 pruned atom pairs is 0.516 angstroms; (across all 366 pairs:
22.197)
> volume #3 level 0.001593
> volume #3 level 0.001285
> hide #!1 models
> hide #!3 models
> show #!3 models
> select clear
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v2.pdb
Chain information for C-terminal_single_subunit_before_coot-v2.pdb #9
---
Chain | Description
B | No description available
> hide #!8 models
> show #!8 models
> ui tool show Matchmaker
> matchmaker #!9 to #8
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 C-terminal_single_subunit_before_coot-v1.pdb, chain B (#8) with
C-terminal_single_subunit_before_coot-v2.pdb, chain B (#9), sequence alignment
score = 1895.5
RMSD between 326 pruned atom pairs is 0.094 angstroms; (across all 368 pairs:
6.667)
> hide #!3 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v3.pdb
Chain information for C-terminal_single_subunit_before_coot-v3.pdb #10
---
Chain | Description
B | No description available
> ui tool show Matchmaker
> matchmaker #!10 to #9
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 C-terminal_single_subunit_before_coot-v2.pdb, chain B (#9) with
C-terminal_single_subunit_before_coot-v3.pdb, chain B (#10), sequence
alignment score = 1895.5
RMSD between 333 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
1.974)
> show #!3 models
> hide #!10 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!8 models
> hide #!3 models
> show #!4 models
> show #!3 models
> show #!10 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> close #8
> close #9
> close #10
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v1.pdb
Chain information for C-terminal_single_subunit_before_coot-v1.pdb #8
---
Chain | Description
B | No description available
> matchmaker #!8 to #5
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 C-terminal.pdb, chain A (#5) with
C-terminal_single_subunit_before_coot-v1.pdb, chain B (#8), sequence alignment
score = 1887.7
RMSD between 326 pruned atom pairs is 0.054 angstroms; (across all 368 pairs:
9.427)
> show #!7 models
> hide #!7 models
> show #!7 models
> matchmaker #!5 to #7
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 C-terminal.pdb, chain B (#7) with C-terminal.pdb, chain A (#5),
sequence alignment score = 1887.7
RMSD between 368 pruned atom pairs is 0.051 angstroms; (across all 368 pairs:
0.051)
> undo
> show #!1 models
> show #!7 models
> select add #7
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.33016,0.70767,0.62465,-95.886,-0.12696,0.62245,-0.77229,47.762,-0.93535,-0.33429,-0.11566,45.843
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.33016,0.70767,0.62465,-27.367,-0.12696,0.62245,-0.77229,23.984,-0.93535,-0.33429,-0.11566,122.02
> view matrix models
> #7,-0.33016,0.70767,0.62465,3.5613,-0.12696,0.62245,-0.77229,129.15,-0.93535,-0.33429,-0.11566,123.46
> view matrix models
> #7,-0.33016,0.70767,0.62465,16.861,-0.12696,0.62245,-0.77229,127.16,-0.93535,-0.33429,-0.11566,114.62
> matchmaker #!7 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 AAT9C5_refine_72.pdb, chain A (#1) with C-terminal.pdb, chain B
(#7), sequence alignment score = 1776.1
RMSD between 328 pruned atom pairs is 0.506 angstroms; (across all 366 pairs:
18.614)
> hide #!5 models
> matchmaker #!8 to #7
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 C-terminal.pdb, chain B (#7) with
C-terminal_single_subunit_before_coot-v1.pdb, chain B (#8), sequence alignment
score = 1896.7
RMSD between 326 pruned atom pairs is 0.001 angstroms; (across all 368 pairs:
9.428)
> view matrix models
> #7,-0.27022,0.91921,0.28641,10.89,0.19623,0.34382,-0.9183,45.095,-0.94259,-0.19194,-0.27329,108.35
> undo
> select subtract #7
Nothing selected
> select add #7.1
2 pseudobonds, 1 model selected
> hide #!1 models
> hide #!4 models
> view matrix models #7.1,1,0,0,0,0,1,0,0,0,0,1,0
> select subtract #7.1
Nothing selected
> ui mousemode right translate
> ui mousemode right zoom
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!7 models
> hide #!3 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v2.pdb
Chain information for C-terminal_single_subunit_before_coot-v2.pdb #9
---
Chain | Description
B | No description available
> matchmaker #!9 to #8
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 C-terminal_single_subunit_before_coot-v1.pdb, chain B (#8) with
C-terminal_single_subunit_before_coot-v2.pdb, chain B (#9), sequence alignment
score = 1889.5
RMSD between 350 pruned atom pairs is 0.328 angstroms; (across all 368 pairs:
0.701)
> show #!3 models
> hide #!8 models
> hide #!3 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v3.pdb
Chain information for C-terminal_single_subunit_before_coot-v3.pdb #10
---
Chain | Description
B | No description available
> matchmaker #!10 to #9
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 C-terminal_single_subunit_before_coot-v2.pdb, chain B (#9) with
C-terminal_single_subunit_before_coot-v3.pdb, chain B (#10), sequence
alignment score = 1835.5
RMSD between 336 pruned atom pairs is 0.198 angstroms; (across all 368 pairs:
1.561)
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!7 models
> hide #!10 models
> hide #!3 models
> close #10
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v3.pdb
Chain information for C-terminal_single_subunit_before_coot-v3.pdb #10
---
Chain | Description
B | No description available
> matchmaker #!10 to #9
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 C-terminal_single_subunit_before_coot-v2.pdb, chain B (#9) with
C-terminal_single_subunit_before_coot-v3.pdb, chain B (#10), sequence
alignment score = 1895.5
RMSD between 331 pruned atom pairs is 0.013 angstroms; (across all 368 pairs:
3.128)
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> hide #!3 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v4.pdb
Chain information for C-terminal_single_subunit_before_coot-v4.pdb #11
---
Chain | Description
B | No description available
> matchmaker #!11 to #10
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 C-terminal_single_subunit_before_coot-v3.pdb, chain B (#10) with
C-terminal_single_subunit_before_coot-v4.pdb, chain B (#11), sequence
alignment score = 1895.5
RMSD between 368 pruned atom pairs is 0.615 angstroms; (across all 368 pairs:
0.615)
> hide #!9 models
> show #!3 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v5.pdb
Chain information for C-terminal_single_subunit_before_coot-v5.pdb #12
---
Chain | Description
B | No description available
> matchmaker #!12 to #11
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 C-terminal_single_subunit_before_coot-v4.pdb, chain B (#11) with
C-terminal_single_subunit_before_coot-v5.pdb, chain B (#12), sequence
alignment score = 1895.5
RMSD between 332 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
1.195)
> hide #!10 models
> hide #!11 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v6.pdb
Chain information for C-terminal_single_subunit_before_coot-v6.pdb #13
---
Chain | Description
B | No description available
> color #13 #ff2600ff
> matchmaker #!13 to #12
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 C-terminal_single_subunit_before_coot-v5.pdb, chain B (#12) with
C-terminal_single_subunit_before_coot-v6.pdb, chain B (#13), sequence
alignment score = 1895.5
RMSD between 329 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
4.628)
> close #13
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v7.pdb
Chain information for C-terminal_single_subunit_before_coot-v7.pdb #13
---
Chain | Description
B | No description available
> matchmaker #!13 to #12
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 C-terminal_single_subunit_before_coot-v5.pdb, chain B (#12) with
C-terminal_single_subunit_before_coot-v7.pdb, chain B (#13), sequence
alignment score = 1895.5
RMSD between 325 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
5.522)
> hide #!12 models
> hide #!3 models
> show #!3 models
> show #!6 models
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.7187,0.021099,-0.695,133.46,0.23517,0.93326,0.27153,-33.031,0.65434,-0.35859,0.66577,67.448
> view matrix models
> #6,0.7187,0.021099,-0.695,132.32,0.23517,0.93326,0.27153,-33.195,0.65434,-0.35859,0.66577,65.258
> view matrix models
> #6,0.7187,0.021099,-0.695,129.18,0.23517,0.93326,0.27153,-33.197,0.65434,-0.35859,0.66577,65.356
> view matrix models
> #6,0.7187,0.021099,-0.695,135.19,0.23517,0.93326,0.27153,-37.095,0.65434,-0.35859,0.66577,71.267
> view matrix models
> #6,0.7187,0.021099,-0.695,126.1,0.23517,0.93326,0.27153,-38.107,0.65434,-0.35859,0.66577,68.464
> view matrix models
> #6,0.7187,0.021099,-0.695,125.53,0.23517,0.93326,0.27153,-35.582,0.65434,-0.35859,0.66577,68.191
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.68537,-0.050132,-0.72647,136.9,0.3578,0.89208,0.27599,-42.336,0.63424,-0.44908,0.62934,80.538
> view matrix models
> #6,0.49795,0.028914,-0.86672,158.68,0.27393,0.94303,0.18884,-31.507,0.8228,-0.33146,0.46166,72.286
> view matrix models
> #6,0.43488,-0.0043966,-0.90048,169.55,0.41257,0.88983,0.1949,-38.706,0.80042,-0.45627,0.38878,91.061
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.43488,-0.0043966,-0.90048,168.97,0.41257,0.88983,0.1949,-32.419,0.80042,-0.45627,0.38878,95.32
> hide #!6 models
> hide #!3 models
> show #!1 models
> hide #!13 models
> show #!3 models
> view matrix models
> #6,0.43488,-0.0043966,-0.90048,185.09,0.41257,0.88983,0.1949,-66.771,0.80042,-0.45627,0.38878,98.107
> select subtract #6
Nothing selected
> select add #6
2 models selected
> show #!7 models
> hide #!7 models
> show #!13 models
> view matrix models
> #6,0.43488,-0.0043966,-0.90048,202.6,0.41257,0.88983,0.1949,-85.845,0.80042,-0.45627,0.38878,101.8
> view matrix models
> #6,0.43488,-0.0043966,-0.90048,217.98,0.41257,0.88983,0.1949,-109.82,0.80042,-0.45627,0.38878,122.59
> select subtract #6
Nothing selected
> show #!6 models
> select add #6
2 models selected
> view matrix models
> #6,0.43488,-0.0043966,-0.90048,172.46,0.41257,0.88983,0.1949,-100.34,0.80042,-0.45627,0.38878,30.485
> view matrix models
> #6,0.43488,-0.0043966,-0.90048,163.31,0.41257,0.88983,0.1949,-33.288,0.80042,-0.45627,0.38878,101.93
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.59843,-0.054875,-0.79929,144.84,0.39509,0.88812,0.23483,-35.595,0.69698,-0.45632,0.55316,94.344
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.59843,-0.054875,-0.79929,149.25,0.39509,0.88812,0.23483,-37.821,0.69698,-0.45632,0.55316,102.14
> view matrix models
> #6,0.59843,-0.054875,-0.79929,147.8,0.39509,0.88812,0.23483,-40.531,0.69698,-0.45632,0.55316,91.114
> view matrix models
> #6,0.59843,-0.054875,-0.79929,148.96,0.39509,0.88812,0.23483,-41.471,0.69698,-0.45632,0.55316,92.483
> view matrix models
> #6,0.59843,-0.054875,-0.79929,143.65,0.39509,0.88812,0.23483,-40.945,0.69698,-0.45632,0.55316,99.081
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.81684,-0.23232,-0.52801,114.81,0.37267,0.9112,0.1756,-35.375,0.44032,-0.34021,0.83089,83.352
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.81684,-0.23232,-0.52801,136.66,0.37267,0.9112,0.1756,-38.435,0.44032,-0.34021,0.83089,73.204
> view matrix models
> #6,0.81684,-0.23232,-0.52801,135.27,0.37267,0.9112,0.1756,-33.729,0.44032,-0.34021,0.83089,71.016
> select subtract #6
Nothing selected
> hide #!6 models
> hide #!3 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v8.pdb
Chain information for C-terminal_single_subunit_before_coot-v8.pdb #14
---
Chain | Description
B | No description available
> matchmaker #!14 to #13
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 C-terminal_single_subunit_before_coot-v7.pdb, chain B (#13) with
C-terminal_single_subunit_before_coot-v8.pdb, chain B (#14), sequence
alignment score = 1895.5
RMSD between 332 pruned atom pairs is 0.018 angstroms; (across all 368 pairs:
2.060)
> hide #!1 models
> show #!3 models
> show #!1 models
> ui mousemode right translate
> ui mousemode right zoom
> hide #!3 models
> show #!3 models
> hide #!3 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v9.pdb
Chain information for C-terminal_single_subunit_before_coot-v9.pdb #15
---
Chain | Description
B | No description available
> matchmaker #!15 to #14
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 C-terminal_single_subunit_before_coot-v8.pdb, chain B (#14) with
C-terminal_single_subunit_before_coot-v9.pdb, chain B (#15), sequence
alignment score = 1895.5
RMSD between 368 pruned atom pairs is 0.500 angstroms; (across all 368 pairs:
0.500)
> show #!3 models
> hide #!13 models
> hide #!14 models
> hide #!1 models
> save /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/Dimer_representation_1.cxs includeMaps true
> hide #!3 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v10.pdb
Chain information for C-terminal_single_subunit_before_coot-v10.pdb #16
---
Chain | Description
B | No description available
> matchmaker #!16 to #15
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 C-terminal_single_subunit_before_coot-v9.pdb, chain B (#15) with
C-terminal_single_subunit_before_coot-v10.pdb, chain B (#16), sequence
alignment score = 1895.5
RMSD between 331 pruned atom pairs is 0.010 angstroms; (across all 368 pairs:
0.964)
> show #!3 models
> hide #!15 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> select #17
Nothing selected
> select #16
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!16 models
> select subtract #16
Nothing selected
> show #!3 models
> hide #!1 models
> color #3 darkgrey models
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> color #3 #a9a9a986 models
> color #3 #929292ff models
> color #3 #797979ff models
> color #3 silver models
> lighting soft
> lighting full
> lighting soft
> color #3 darkgrey models
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> graphics silhouettes true
> color #3 darkgrey models
> color #3 #929292ff models
> ui tool show "Side View"
> color #3 #009051ff models
> color #3 darkgrey models
> color #3 #929292ff models
> color #3 darkgrey models
> lighting full
> color #3 #a9a9a9ef models
> color #3 darkgrey models
> show #!1 models
> color #3 #a9a9a969 models
> hide #!1 models
> save /Users/ibrahim/Desktop/image189.png supersample 3
> show #!1 models
> save /Users/ibrahim/Desktop/image190.png supersample 3
> hide #!1 models
> color #3 darkgrey models
> hide #!3 models
> show #!3 models
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting simple
> lighting soft
> lighting flat
> ui mousemode right translate
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> show #!16 models
> hide #!16 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> color #3 darkgrey models
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting full
> save /Users/ibrahim/Desktop/image189.png supersample 3
> color #3 #a9a9a979 models
> color #3 #a9a9a95c models
> color #3 #a9a9a967 models
> show #!16 models
> lighting soft
> select #16
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> color #3 #7a81ffff models
> color #3 darkgrey models
> hide #!16 models
> save /Users/ibrahim/Desktop/image189.png supersample 3
> select subtract #16
Nothing selected
> color #3 #a9a9a9b9 models
> color #3 #a9a9a95f models
> color #3 #a9a9a965 models
> show #!16 models
> show #!1 models
> hide #!3 models
> hide #!16 models
> select #1/A
2891 atoms, 2950 bonds, 369 residues, 1 model selected
> hide sel cartoons
> show #!16 models
> show #!3 models
> color #3 #7a81ffff models
> color #3 darkgrey models
> color #3 #a9a9a980 models
> color #3 #a9a9a960 models
> color #3 #a9a9a950 models
> color #3 #a9a9a966 models
> color #16 mediumslateblue
> select #16
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> select helix
11382 atoms, 11455 bonds, 1434 residues, 12 models selected
> select clear
> hide #!1 models
> show #!1 models
> select #16 helix
Expected a keyword
> select #16/A helix
Expected a keyword
> select #16/b helix
Expected a keyword
> select #16 /B
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> hide #!1 models
> select #16 /B
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> select #16 /B HELIX
Expected a keyword
> select #16 /B helix
Expected a keyword
> select #16 /B helix
Expected a keyword
> save /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/Dimer_representation_CterminalMechanism.cxs includeMaps
> true
> select #16 /B helix
Expected a keyword
> select #16 /B
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> hide #!3 models
> close #15
> close #14
> close #13
> close #12
> close #11
> close #10
> close #9
> close #8
> show #!7 models
> hide #!7 models
> show #7.1 models
> hide #!7 models
> show #!7 models
> show #!5 models
> hide #!5 models
> close #7
> select #16 /B
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> select helix
3669 atoms, 3688 bonds, 462 residues, 3 models selected
> select add #1
8738 atoms, 8897 bonds, 1121 residues, 3 models selected
> select subtract #1
2571 atoms, 2589 bonds, 324 residues, 2 models selected
> select add #5
6603 atoms, 6725 bonds, 4 pseudobonds, 844 residues, 3 models selected
> select subtract #5
857 atoms, 863 bonds, 108 residues, 1 model selected
> color sel yellow
> select #16 /B:341-357
122 atoms, 123 bonds, 17 residues, 1 model selected
> color sel red
> select #16 /B:358-394
290 atoms, 298 bonds, 37 residues, 1 model selected
> show #!3 models
> color sel forest green
> select clear
> show #!1 models
> select #16 /B:358-394
290 atoms, 298 bonds, 37 residues, 1 model selected
> color sel dark gray
> color sel orange
> color sel magenta
> select clear
> show #!6 models
> ui mousemode right zoom
> select add #16
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> select subtract #16
Nothing selected
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.81684,-0.23232,-0.52801,137.39,0.37267,0.9112,0.1756,-33.827,0.44032,-0.34021,0.83089,70.098
> view matrix models
> #6,0.81684,-0.23232,-0.52801,139.07,0.37267,0.9112,0.1756,-31.775,0.44032,-0.34021,0.83089,72.018
> view matrix models
> #6,0.81684,-0.23232,-0.52801,139.1,0.37267,0.9112,0.1756,-32.107,0.44032,-0.34021,0.83089,72.098
> view matrix models
> #6,0.81684,-0.23232,-0.52801,132.56,0.37267,0.9112,0.1756,-130.11,0.44032,-0.34021,0.83089,75.38
> vop add #16
> vop copy #16
> show #!5 models
> view matrix models
> #6,0.81684,-0.23232,-0.52801,135.33,0.37267,0.9112,0.1756,-130.16,0.44032,-0.34021,0.83089,78.595
> select subtract #6
Nothing selected
> hide #!5 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> open /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/C-terminal_single_subunit_before_coot-v10.pdb
Chain information for C-terminal_single_subunit_before_coot-v10.pdb #7
---
Chain | Description
B | No description available
> select add #7
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.227,0.25019,-0.94121,-25.798,0.93929,-0.19909,-0.27946,99.307,-0.25731,-0.9475,-0.18981,73.549
> view matrix models
> #7,0.79272,-0.32019,-0.51873,24.262,0.52113,0.79743,0.30417,18.561,0.31626,-0.51145,0.799,41.942
> view matrix models
> #7,-0.3539,0.59747,-0.71958,-53.844,0.71504,-0.32311,-0.61994,107.99,-0.60289,-0.73392,-0.31286,54.982
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.3539,0.59747,-0.71958,35.171,0.71504,-0.32311,-0.61994,135.14,-0.60289,-0.73392,-0.31286,168.22
> view matrix models
> #7,-0.3539,0.59747,-0.71958,94.05,0.71504,-0.32311,-0.61994,162.59,-0.60289,-0.73392,-0.31286,106.6
> view matrix models
> #7,-0.3539,0.59747,-0.71958,100.58,0.71504,-0.32311,-0.61994,172.98,-0.60289,-0.73392,-0.31286,104.1
> view matrix models
> #7,-0.3539,0.59747,-0.71958,76.624,0.71504,-0.32311,-0.61994,168.9,-0.60289,-0.73392,-0.31286,115.06
> view matrix models
> #7,-0.3539,0.59747,-0.71958,76.445,0.71504,-0.32311,-0.61994,169.32,-0.60289,-0.73392,-0.31286,137.24
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.18888,0.93524,-0.2994,63.302,0.65478,-0.34717,-0.67137,170.16,-0.73184,-0.069233,-0.67795,106.25
> matchmaker #!7 to #16
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 C-terminal_single_subunit_before_coot-v10.pdb, chain B (#16) with
C-terminal_single_subunit_before_coot-v10.pdb, chain B (#7), sequence
alignment score = 1895.5
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.014187,0.86596,-0.49991,-0.35777,0.99587,-0.0326,-0.084732,148.63,-0.089672,-0.49905,-0.86192,101.5
> view matrix models
> #7,-0.014187,0.86596,-0.49991,1.662,0.99587,-0.0326,-0.084732,155.87,-0.089672,-0.49905,-0.86192,111.06
> view matrix models
> #7,-0.014187,0.86596,-0.49991,0.89539,0.99587,-0.0326,-0.084732,156.6,-0.089672,-0.49905,-0.86192,110.6
> view matrix models
> #7,-0.014187,0.86596,-0.49991,0.077221,0.99587,-0.0326,-0.084732,157.03,-0.089672,-0.49905,-0.86192,109.98
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.11648,0.8344,-0.53871,-0.19012,0.99318,0.095025,-0.067569,149.57,-0.0051879,-0.54291,-0.83978,114.26
> view matrix models
> #7,0.18099,0.78667,-0.59025,12.241,0.94742,0.021574,0.31927,142.75,0.26389,-0.617,-0.7414,123.62
> view matrix models
> #7,0.14496,0.77488,-0.61527,12.463,0.93956,0.087146,0.33111,138.65,0.31019,-0.62607,-0.71541,124.81
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.14496,0.77488,-0.61527,1.621,0.93956,0.087146,0.33111,145.21,0.31019,-0.62607,-0.71541,135.01
> view matrix models
> #7,0.14496,0.77488,-0.61527,8.5446,0.93956,0.087146,0.33111,133.45,0.31019,-0.62607,-0.71541,135.12
> view matrix models
> #7,0.14496,0.77488,-0.61527,106.44,0.93956,0.087146,0.33111,105.92,0.31019,-0.62607,-0.71541,192.96
> view matrix models
> #7,0.14496,0.77488,-0.61527,99.285,0.93956,0.087146,0.33111,85.285,0.31019,-0.62607,-0.71541,183.33
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.043554,-0.088572,-0.99512,150.3,-0.8244,-0.55945,0.085877,75.829,-0.56433,0.82412,-0.048652,62.658
> view matrix models
> #7,-0.0085734,-0.047852,-0.99882,149.18,-0.79274,-0.60849,0.035957,80.643,-0.6095,0.79211,-0.032717,62.712
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.0085734,-0.047852,-0.99882,71.358,-0.79274,-0.60849,0.035957,137.8,-0.6095,0.79211,-0.032717,2.4202
> view matrix models
> #7,-0.0085734,-0.047852,-0.99882,69.971,-0.79274,-0.60849,0.035957,148.91,-0.6095,0.79211,-0.032717,6.5201
> vop copy #7:1-360
> select #7: 1-360
2608 atoms, 2657 bonds, 2 pseudobonds, 334 residues, 2 models selected
> select #7: 1-356
2576 atoms, 2624 bonds, 2 pseudobonds, 330 residues, 2 models selected
> select #7: 1-357
2583 atoms, 2632 bonds, 2 pseudobonds, 331 residues, 2 models selected
> hide sel cartoons
> color #7 #941751ff
> color #7 #00f900ff
> color #7 #ff40ffff
> select add #7
2873 atoms, 2931 bonds, 2 pseudobonds, 368 residues, 2 models selected
> view matrix models
> #7,-0.0085734,-0.047852,-0.99882,64.382,-0.79274,-0.60849,0.035957,147.7,-0.6095,0.79211,-0.032717,14.687
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.052498,-0.049908,-0.99737,63.532,-0.81985,-0.56809,0.07158,144.19,-0.57017,0.82145,-0.011094,13.477
> view matrix models
> #7,0.00066475,-0.10869,-0.99408,69.021,-0.78392,-0.61724,0.066964,148.58,-0.62086,0.77923,-0.085617,15.3
> view matrix models
> #7,0.28793,-0.085082,-0.95386,73.903,-0.88028,-0.41574,-0.22863,131.38,-0.3771,0.9055,-0.1946,11.548
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.28793,-0.085082,-0.95386,72.45,-0.88028,-0.41574,-0.22863,125.18,-0.3771,0.9055,-0.1946,7.5666
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.48552,-0.1273,-0.86491,80.131,-0.69254,-0.65979,-0.29165,147.13,-0.53353,0.74059,-0.4085,15.731
> view matrix models
> #7,0.5161,-0.13708,-0.84548,81.563,-0.68381,-0.66037,-0.31035,147.35,-0.51579,0.73832,-0.43456,16.269
> view matrix models
> #7,0.47604,-0.12853,-0.86998,79.998,-0.70497,-0.64717,-0.29014,145.93,-0.52573,0.75143,-0.39869,15.132
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.47604,-0.12853,-0.86998,81.44,-0.70497,-0.64717,-0.29014,145.73,-0.52573,0.75143,-0.39869,16.017
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.47604,-0.12853,-0.86998,82.98,-0.70497,-0.64717,-0.29014,146.63,-0.52573,0.75143,-0.39869,14.994
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.47604,-0.12853,-0.86998,81.566,-0.70497,-0.64717,-0.29014,145.56,-0.52573,0.75143,-0.39869,12.97
> select #7: 1-357
2583 atoms, 2632 bonds, 2 pseudobonds, 331 residues, 2 models selected
> show sel cartoons
> select #7: 357-394
297 atoms, 306 bonds, 38 residues, 1 model selected
> color sel hot pink
> color sel cyan
> select clear
> select #7: 1-356
2576 atoms, 2624 bonds, 2 pseudobonds, 330 residues, 2 models selected
> color #7 mediumslateblue
> select clear
> select #7: 1-356
2576 atoms, 2624 bonds, 2 pseudobonds, 330 residues, 2 models selected
> select helix
4526 atoms, 4551 bonds, 570 residues, 4 models selected
> select add #16
6542 atoms, 6619 bonds, 2 pseudobonds, 830 residues, 5 models selected
> select subtract #16
3669 atoms, 3688 bonds, 462 residues, 3 models selected
> select add #5
7701 atoms, 7824 bonds, 4 pseudobonds, 982 residues, 4 models selected
> select subtract #5
1955 atoms, 1962 bonds, 246 residues, 2 models selected
> select add #1
7024 atoms, 7171 bonds, 905 residues, 2 models selected
> select subtract #1
857 atoms, 863 bonds, 108 residues, 1 model selected
> color sel yellow
> select #7: 341-357
122 atoms, 123 bonds, 17 residues, 1 model selected
> color sel red
> select #7: 357-394
297 atoms, 306 bonds, 38 residues, 1 model selected
> select #7: 358-394
290 atoms, 298 bonds, 37 residues, 1 model selected
> color sel magenta
> select clear
> save /Users/ibrahim/Desktop/AAT_cryo-EM_paper/CRYO-
> emFigures/fIGURE2/Dimer_representation_CterminalMechanism.cxs includeMaps
> true
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
OS Loader Version: 564.40.4~66
Software:
System Software Overview:
System Version: macOS 13.2 (22D49)
Kernel Version: Darwin 22.3.0
Time since boot: 41 days, 12 hours, 56 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG ULTRAFINE:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 109NTMXM4267
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
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 , 16 months ago
| 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 , 16 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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