![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9928 closed defect (nonchimerax)
Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 655
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5rc202211182308 (2022-11-18 23:08:37 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff84e66f4c0 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1647 in set_multishadow_view
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 239 in _draw_scene
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 177 in draw
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 300000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 1127,
"osVersion" : {
"train" : "macOS 13.0.1",
"build" : "22A400",
"releaseType" : "User"
},
"captureTime" : "2023-10-08 16:13:13.2200 +0200",
"incident" : "AD2EFDD4-982D-4A67-8E0B-96873BCF3ECF",
"pid" : 52603,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-10-08 15:47:41.7390 +0200",
"procStartAbsTime" : 304040355125521,
"procExitAbsTime" : 305571839378354,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"4118825E-EA91-5E09-A29F-34B7D8399597","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "DAE5A66E-5B02-652B-9AB4-D1348B2E5EC8",
"wakeTime" : 2456,
"bridgeVersion" : {"build":"20P420","train":"7.0"},
"sleepWakeUUID" : "5D4015F2-A9FE-4E85-AE63-507327750F44",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
"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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"base" : 140707827527680,
"size" : 45048,
"uuid" : "7d9c3a7b-8be1-3221-b85d-a05c3a505598",
"path" : "\/System\/Library\/PrivateFrameworks\/GPUSupport.framework\/Versions\/A\/Libraries\/libGPUSupportMercury.dylib",
"name" : "libGPUSupportMercury.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712116416512,
"CFBundleShortVersionString" : "20.2.44",
"CFBundleIdentifier" : "com.apple.driver.AppleIntelKBLGraphicsGLDriver",
"size" : 16039936,
"uuid" : "6aaee0c0-2a74-385e-b06f-2d22812274fa",
"path" : "\/System\/Library\/Extensions\/AppleIntelKBLGraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelKBLGraphicsGLDriver",
"name" : "AppleIntelKBLGraphicsGLDriver",
"CFBundleVersion" : "20.0.2"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712241872896,
"size" : 1613816,
"uuid" : "72abfc77-407e-360a-9db4-05d8f10be643",
"path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Resources\/GLEngine.bundle\/GLEngine",
"name" : "GLEngine"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703566897152,
"size" : 24544,
"uuid" : "fcf97ef0-dbaf-333c-b3de-663c59f2d727",
"path" : "\/usr\/lib\/libffi.dylib",
"name" : "libffi.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4440457216,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4952887296,
"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
"path" : "\/Applications\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703310675968,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4820992,
"uuid" : "dbc459f3-81bb-398a-8f74-3f7392392bb7",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1953.1"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703362453504,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16797687,
"uuid" : "817d572e-eb8c-3999-b7a0-68e1c4b47266",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299"
}
],
"sharedCache" : {
"base" : 140703306321920,
"size" : 21474836480,
"uuid" : "840e528a-0c70-3c6a-b7b4-4f05f32ccc51"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63a0a6cfd1cdb67d083006d0",
"factorPackIds" : {
},
"deploymentId" : 240000003
},
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000014
}
],
"experiments" : [
{
"treatmentId" : "6dd670af-0633-45e4-ae5f-122ae4df02be",
"experimentId" : "64406ba83deb637ac8a04419",
"deploymentId" : 900000017
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5rc202211182308 (2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP_preholo_v2/ChimeraX/Structure_20SCP_preholo_model_building.cxs
Opened cryosparc_P109_J413_map_sharp.mrc as #1, grid size 168,168,168, pixel
1.88, shown at level 0.126, step 1, values float32
Log from Wed Oct 4 16:50:44 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/fadlof/Downloads/ModelBuilding/Old_ModelBuilding_preholo-20SCP/ChimeraX_scessions/Structure_20SCP_preholo_model_building.cxs
Opened cryosparc_P231_J120_preholo_manual_sharp_deepEmhancer.mrc as #3, grid
size 168,168,168, pixel 1.88, shown at level 0.095, step 1, values float32
Log from Mon Oct 2 19:49:22 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_preholo-20SCP/ChimeraX_scessions/Structure_20SCP_preholo_model_building.cxs
Opened cryosparc_P231_J120_preholo_manual_sharp_deepEmhancer.mrc as #1, grid
size 168,168,168, pixel 1.88, shown at level 0.095, step 1, values float32
Log from Thu Sep 21 14:08:58 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/fadlof/Downloads/20SCP_preholo/ChimeraX_scessions/Structure_20SCP_preholo_model_building.cxs
Opened cryosparc_P231_J120_preholo_manual_sharp_deepEmhancer.mrc as #1, grid
size 168,168,168, pixel 1.88, shown at level 0.172, step 1, values float32
Log from Tue Sep 19 12:38:57 2023UCSF ChimeraX version: 1.5rc202211182308
(2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/fadlof/Downloads/20SCP_preholo/Structure_20SCP_preholo_docking.pdb
Chain information for Structure_20SCP_preholo_docking.pdb #1
---
Chain | Description
A R | No description available
B S | No description available
C T | No description available
D U | No description available
E V | No description available
F W | No description available
G X | No description available
H Y | No description available
I Z | No description available
J a | No description available
K b | No description available
L c | No description available
M d | No description available
N e | No description available
O f | No description available
P g | No description available
Q h | No description available
> open /Users/fadlof/Downloads/20SCP_preholo/Structure_20SCP.pdb
Chain information for Structure_20SCP.pdb #2
---
Chain | Description
A O | No description available
B P | No description available
C Q | No description available
D R | No description available
E S | No description available
F T | No description available
G U | No description available
H V | No description available
I W | No description available
J X | No description available
K Y | No description available
L Z | No description available
M a | No description available
N b | No description available
> open
> /Users/fadlof/Downloads/20SCP_preholo/cryosparc_P231_J111_preholo_map_auto_sharp.mrc
Opened cryosparc_P231_J111_preholo_map_auto_sharp.mrc as #3, grid size
168,168,168, pixel 1.88, shown at level 0.701, step 1, values float32
> open
> /Users/fadlof/Downloads/20SCP_preholo/cryosparc_P231_J111_preholo_map.mrc
Opened cryosparc_P231_J111_preholo_map.mrc as #4, grid size 168,168,168, pixel
1.88, shown at level 0.566, step 1, values float32
> open
> /Users/fadlof/Downloads/20SCP_preholo/cryosparc_P231_J118_preholo_auto_sharp_deepEmhancer.mrc
Opened cryosparc_P231_J118_preholo_auto_sharp_deepEmhancer.mrc as #5, grid
size 168,168,168, pixel 1.88, shown at level 0.114, step 1, values float32
> open
> /Users/fadlof/Downloads/20SCP_preholo/cryosparc_P231_J119_preholo_map_manual_sharp.mrc
Opened cryosparc_P231_J119_preholo_map_manual_sharp.mrc as #6, grid size
168,168,168, pixel 1.88, shown at level 0.643, step 1, values float32
> open
> /Users/fadlof/Downloads/20SCP_preholo/cryosparc_P231_J120_preholo_manual_sharp_deepEmhancer.mrc
Opened cryosparc_P231_J120_preholo_manual_sharp_deepEmhancer.mrc as #7, grid
size 168,168,168, pixel 1.88, shown at level 0.128, step 1, values float32
> set bgColor white
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> hide atoms
> show cartoons
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #2
48138 atoms, 49002 bonds, 2 pseudobonds, 6222 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.65458,0.60451,0.45398,-120.37,-0.12097,0.67652,-0.72642,197.57,-0.74625,0.42058,0.51597,136.54
> view matrix models
> #2,0.12256,0.98523,0.11957,-38.229,0.6628,0.0084217,-0.74875,182.24,-0.7387,0.17102,-0.65198,376.05
> view matrix models
> #2,-0.1587,0.78422,0.59985,-40.532,0.78866,0.4662,-0.40085,26.322,-0.594,0.40946,-0.69246,319.62
> view matrix models
> #2,-0.25401,0.89761,0.36025,-2.5906,0.84155,0.38869,-0.3751,25.992,-0.47672,0.20789,-0.85412,361.17
> view matrix models
> #2,0.033257,0.99943,0.0059249,-6.3985,0.82662,-0.024173,-0.56223,128.68,-0.56177,0.023596,-0.82696,401.06
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.033257,0.99943,0.0059249,-18.925,0.82662,-0.024173,-0.56223,112.46,-0.56177,0.023596,-0.82696,403.14
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.47872,0.7678,-0.4258,177.77,0.87622,0.3872,-0.28692,-10.78,-0.055429,-0.51044,-0.85812,413.04
> view matrix models
> #2,-0.37483,0.92396,-0.076183,75.052,0.91252,0.3822,0.14571,-89.856,0.16375,-0.014903,-0.98639,316.78
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.37483,0.92396,-0.076183,77.126,0.91252,0.3822,0.14571,-75.547,0.16375,-0.014903,-0.98639,311.9
> ui tool show "Fit in Map"
> fitmap #2 inMap #3
Fit molecule Structure_20SCP.pdb (#2) to map
cryosparc_P231_J111_preholo_map_auto_sharp.mrc (#3) using 48138 atoms
average map value = 0.8409, steps = 84
shifted from previous position = 6.85
rotated from previous position = 10.1 degrees
atoms outside contour = 19008, contour level = 0.70134
Position of Structure_20SCP.pdb (#2) relative to
cryosparc_P231_J111_preholo_map_auto_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.43603141 0.89993144 0.00002085 81.62106561
0.89993144 0.43603141 0.00000761 -62.56733014
-0.00000224 0.00002208 -1.00000000 341.51039108
Axis 0.53100528 0.84736851 0.00000595
Axis point 60.41588101 0.00000000 170.75506650
Rotation angle (degrees) 179.99921932
Shift along axis -9.67433581
> select subtract #2
Nothing selected
> hide #!3 models
> split #2
Split Structure_20SCP.pdb (#2) into 28 models
Chain information for Structure_20SCP.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for Structure_20SCP.pdb B #2.2
---
Chain | Description
B | No description available
Chain information for Structure_20SCP.pdb C #2.3
---
Chain | Description
C | No description available
Chain information for Structure_20SCP.pdb D #2.4
---
Chain | Description
D | No description available
Chain information for Structure_20SCP.pdb E #2.5
---
Chain | Description
E | No description available
Chain information for Structure_20SCP.pdb F #2.6
---
Chain | Description
F | No description available
Chain information for Structure_20SCP.pdb G #2.7
---
Chain | Description
G | No description available
Chain information for Structure_20SCP.pdb H #2.8
---
Chain | Description
H | No description available
Chain information for Structure_20SCP.pdb I #2.9
---
Chain | Description
I | No description available
Chain information for Structure_20SCP.pdb J #2.10
---
Chain | Description
J | No description available
Chain information for Structure_20SCP.pdb K #2.11
---
Chain | Description
K | No description available
Chain information for Structure_20SCP.pdb L #2.12
---
Chain | Description
L | No description available
Chain information for Structure_20SCP.pdb M #2.13
---
Chain | Description
M | No description available
Chain information for Structure_20SCP.pdb N #2.14
---
Chain | Description
N | No description available
Chain information for Structure_20SCP.pdb O #2.15
---
Chain | Description
O | No description available
Chain information for Structure_20SCP.pdb P #2.16
---
Chain | Description
P | No description available
Chain information for Structure_20SCP.pdb Q #2.17
---
Chain | Description
Q | No description available
Chain information for Structure_20SCP.pdb R #2.18
---
Chain | Description
R | No description available
Chain information for Structure_20SCP.pdb S #2.19
---
Chain | Description
S | No description available
Chain information for Structure_20SCP.pdb T #2.20
---
Chain | Description
T | No description available
Chain information for Structure_20SCP.pdb U #2.21
---
Chain | Description
U | No description available
Chain information for Structure_20SCP.pdb V #2.22
---
Chain | Description
V | No description available
Chain information for Structure_20SCP.pdb W #2.23
---
Chain | Description
W | No description available
Chain information for Structure_20SCP.pdb X #2.24
---
Chain | Description
X | No description available
Chain information for Structure_20SCP.pdb Y #2.25
---
Chain | Description
Y | No description available
Chain information for Structure_20SCP.pdb Z #2.26
---
Chain | Description
Z | No description available
Chain information for Structure_20SCP.pdb a #2.27
---
Chain | Description
a | No description available
Chain information for Structure_20SCP.pdb b #2.28
---
Chain | Description
b | No description available
> split #1
Split Structure_20SCP_preholo_docking.pdb (#1) into 34 models
Chain information for Structure_20SCP_preholo_docking.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for Structure_20SCP_preholo_docking.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for Structure_20SCP_preholo_docking.pdb C #1.3
---
Chain | Description
C | No description available
Chain information for Structure_20SCP_preholo_docking.pdb D #1.4
---
Chain | Description
D | No description available
Chain information for Structure_20SCP_preholo_docking.pdb E #1.5
---
Chain | Description
E | No description available
Chain information for Structure_20SCP_preholo_docking.pdb F #1.6
---
Chain | Description
F | No description available
Chain information for Structure_20SCP_preholo_docking.pdb G #1.7
---
Chain | Description
G | No description available
Chain information for Structure_20SCP_preholo_docking.pdb H #1.8
---
Chain | Description
H | No description available
Chain information for Structure_20SCP_preholo_docking.pdb I #1.9
---
Chain | Description
I | No description available
Chain information for Structure_20SCP_preholo_docking.pdb J #1.10
---
Chain | Description
J | No description available
Chain information for Structure_20SCP_preholo_docking.pdb K #1.11
---
Chain | Description
K | No description available
Chain information for Structure_20SCP_preholo_docking.pdb L #1.12
---
Chain | Description
L | No description available
Chain information for Structure_20SCP_preholo_docking.pdb M #1.13
---
Chain | Description
M | No description available
Chain information for Structure_20SCP_preholo_docking.pdb N #1.14
---
Chain | Description
N | No description available
Chain information for Structure_20SCP_preholo_docking.pdb O #1.15
---
Chain | Description
O | No description available
Chain information for Structure_20SCP_preholo_docking.pdb P #1.16
---
Chain | Description
P | No description available
Chain information for Structure_20SCP_preholo_docking.pdb Q #1.17
---
Chain | Description
Q | No description available
Chain information for Structure_20SCP_preholo_docking.pdb R #1.18
---
Chain | Description
R | No description available
Chain information for Structure_20SCP_preholo_docking.pdb S #1.19
---
Chain | Description
S | No description available
Chain information for Structure_20SCP_preholo_docking.pdb T #1.20
---
Chain | Description
T | No description available
Chain information for Structure_20SCP_preholo_docking.pdb U #1.21
---
Chain | Description
U | No description available
Chain information for Structure_20SCP_preholo_docking.pdb V #1.22
---
Chain | Description
V | No description available
Chain information for Structure_20SCP_preholo_docking.pdb W #1.23
---
Chain | Description
W | No description available
Chain information for Structure_20SCP_preholo_docking.pdb X #1.24
---
Chain | Description
X | No description available
Chain information for Structure_20SCP_preholo_docking.pdb Y #1.25
---
Chain | Description
Y | No description available
Chain information for Structure_20SCP_preholo_docking.pdb Z #1.26
---
Chain | Description
Z | No description available
Chain information for Structure_20SCP_preholo_docking.pdb a #1.27
---
Chain | Description
a | No description available
Chain information for Structure_20SCP_preholo_docking.pdb b #1.28
---
Chain | Description
b | No description available
Chain information for Structure_20SCP_preholo_docking.pdb c #1.29
---
Chain | Description
c | No description available
Chain information for Structure_20SCP_preholo_docking.pdb d #1.30
---
Chain | Description
d | No description available
Chain information for Structure_20SCP_preholo_docking.pdb e #1.31
---
Chain | Description
e | No description available
Chain information for Structure_20SCP_preholo_docking.pdb f #1.32
---
Chain | Description
f | No description available
Chain information for Structure_20SCP_preholo_docking.pdb g #1.33
---
Chain | Description
g | No description available
Chain information for Structure_20SCP_preholo_docking.pdb h #1.34
---
Chain | Description
h | No description available
> close #3
> close #4
> close #5
> close #6
> color #7 silver models
> show #!7 models
> hide #!7 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> select add #1.1
1727 atoms, 1766 bonds, 229 residues, 1 model selected
> show #1.1 models
> show #!1.2 models
> select add #1.2
3489 atoms, 3555 bonds, 1 pseudobond, 471 residues, 3 models selected
> show #1.3 models
> select add #1.3
5221 atoms, 5310 bonds, 1 pseudobond, 704 residues, 4 models selected
> show #!1.4 models
> select add #1.4
6968 atoms, 7085 bonds, 2 pseudobonds, 939 residues, 6 models selected
> show #1.5 models
> select add #1.5
8800 atoms, 8952 bonds, 2 pseudobonds, 1177 residues, 7 models selected
> show #1.6 models
> select add #1.6
10634 atoms, 10821 bonds, 2 pseudobonds, 1417 residues, 8 models selected
> show #1.7 models
> select add #1.7
12472 atoms, 12692 bonds, 2 pseudobonds, 1661 residues, 9 models selected
> show #1.8 models
> select add #1.8
13373 atoms, 13608 bonds, 2 pseudobonds, 1774 residues, 10 models selected
> show #!1.9 models
> select add #1.9
15367 atoms, 15644 bonds, 5 pseudobonds, 2038 residues, 12 models selected
> show #!1.10 models
> select add #1.10
17250 atoms, 17567 bonds, 7 pseudobonds, 2286 residues, 14 models selected
> show #!1.11 models
> select add #1.11
18887 atoms, 19232 bonds, 10 pseudobonds, 2515 residues, 16 models selected
> hide #!1.11 models
> select subtract #1.11
17250 atoms, 17567 bonds, 7 pseudobonds, 2286 residues, 14 models selected
> show #!1.17 models
> select add #1.17
18669 atoms, 19011 bonds, 10 pseudobonds, 2476 residues, 16 models selected
> select subtract #1.17
17250 atoms, 17567 bonds, 7 pseudobonds, 2286 residues, 14 models selected
> hide #!1.17 models
> show #!1.11 models
> select add #1.11
18887 atoms, 19232 bonds, 10 pseudobonds, 2515 residues, 16 models selected
> show #1.18 models
> select add #1.18
20614 atoms, 20998 bonds, 10 pseudobonds, 2744 residues, 17 models selected
> hide #!2 models
> show #!1.19 models
> select add #1.19
22376 atoms, 22787 bonds, 11 pseudobonds, 2986 residues, 19 models selected
> show #1.20 models
> select add #1.20
24108 atoms, 24542 bonds, 11 pseudobonds, 3219 residues, 20 models selected
> show #!1.21 models
> select add #1.21
25855 atoms, 26317 bonds, 12 pseudobonds, 3454 residues, 22 models selected
> show #1.22 models
> select add #1.22
27687 atoms, 28184 bonds, 12 pseudobonds, 3692 residues, 23 models selected
> show #1.23 models
> select add #1.23
29521 atoms, 30053 bonds, 12 pseudobonds, 3932 residues, 24 models selected
> show #1.24 models
> select add #1.24
31359 atoms, 31924 bonds, 12 pseudobonds, 4176 residues, 25 models selected
> show #1.25 models
> select add #1.25
32260 atoms, 32840 bonds, 12 pseudobonds, 4289 residues, 26 models selected
> show #!1.26 models
> select add #1.26
34254 atoms, 34876 bonds, 15 pseudobonds, 4553 residues, 28 models selected
> show #!1.27 models
> select add #1.27
36137 atoms, 36799 bonds, 17 pseudobonds, 4801 residues, 30 models selected
> show #!1.28 models
> hide #!1.28 models
> show #!1.28 models
> hide #2.1 models
> show #!2 models
> hide #!2 models
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> hide #2.2 models
> hide #!2 models
> hide #!2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> hide #2.8 models
> hide #2.9 models
> hide #2.10 models
> hide #2.11 models
> hide #2.12 models
> hide #2.13 models
> hide #2.14 models
> hide #2.15 models
> hide #2.16 models
> hide #2.17 models
> hide #!2.18 models
> hide #2.19 models
> hide #2.20 models
> hide #2.21 models
> hide #2.22 models
> hide #2.23 models
> hide #2.24 models
> hide #2.25 models
> hide #2.26 models
> hide #2.27 models
> hide #2.28 models
> show #2.1 models
> hide #2.1 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> select add #2.9
37728 atoms, 38419 bonds, 17 pseudobonds, 5005 residues, 31 models selected
> show #2.10 models
> select add #2.10
39289 atoms, 40012 bonds, 17 pseudobonds, 5201 residues, 32 models selected
> show #2.11 models
> select add #2.11
40832 atoms, 41586 bonds, 17 pseudobonds, 5402 residues, 33 models selected
> show #2.12 models
> select add #2.12
42482 atoms, 43266 bonds, 17 pseudobonds, 5615 residues, 34 models selected
> show #2.13 models
> select add #2.13
44168 atoms, 44985 bonds, 17 pseudobonds, 5831 residues, 35 models selected
> show #2.14 models
> select add #2.14
45682 atoms, 46526 bonds, 17 pseudobonds, 6034 residues, 36 models selected
> show #2.15 models
> hide #2.15 models
> show #2.22 models
> hide #2.22 models
> show #2.22 models
> hide #2.22 models
> show #2.22 models
> hide #2.22 models
> show #2.22 models
> hide #2.22 models
> show #2.22 models
> hide #2.22 models
> show #2.23 models
> select add #2.23
47273 atoms, 48146 bonds, 17 pseudobonds, 6238 residues, 37 models selected
> show #2.24 models
> select add #2.24
48834 atoms, 49739 bonds, 17 pseudobonds, 6434 residues, 38 models selected
> show #2.25 models
> select add #2.25
50377 atoms, 51313 bonds, 17 pseudobonds, 6635 residues, 39 models selected
> show #2.26 models
> select add #2.26
52027 atoms, 52993 bonds, 17 pseudobonds, 6848 residues, 40 models selected
> show #2.27 models
> select add #2.27
53713 atoms, 54712 bonds, 17 pseudobonds, 7064 residues, 41 models selected
> show #2.28 models
> select add #2.28
55227 atoms, 56253 bonds, 17 pseudobonds, 7267 residues, 42 models selected
> hide #!1.11 models
> show #!1.11 models
> hide #!1.11 models
> show #!1.11 models
> hide #!1.11 models
> select subtract #1.11
53590 atoms, 54588 bonds, 14 pseudobonds, 7038 residues, 40 models selected
> hide #!1.28 models
> show #2.15 models
> select add #2.15
55365 atoms, 56402 bonds, 14 pseudobonds, 7267 residues, 41 models selected
> select subtract #2.15
53590 atoms, 54588 bonds, 14 pseudobonds, 7038 residues, 40 models selected
> select add #2.15
55365 atoms, 56402 bonds, 14 pseudobonds, 7267 residues, 41 models selected
> select subtract #2.15
53590 atoms, 54588 bonds, 14 pseudobonds, 7038 residues, 40 models selected
> hide #2.15 models
> show #2.8 models
> select add #2.8
55249 atoms, 56274 bonds, 14 pseudobonds, 7258 residues, 41 models selected
> show #2.22 models
> select add #2.22
56908 atoms, 57960 bonds, 14 pseudobonds, 7478 residues, 42 models selected
> combine sel
Remapping chain ID 'H' in Structure_20SCP.pdb H #2.8 to 'K'
Remapping chain ID 'I' in Structure_20SCP.pdb I #2.9 to 'L'
Remapping chain ID 'J' in Structure_20SCP.pdb J #2.10 to 'M'
Remapping chain ID 'K' in Structure_20SCP.pdb K #2.11 to 'N'
Remapping chain ID 'L' in Structure_20SCP.pdb L #2.12 to 'O'
Remapping chain ID 'M' in Structure_20SCP.pdb M #2.13 to 'P'
Remapping chain ID 'N' in Structure_20SCP.pdb N #2.14 to 'Q'
Remapping chain ID 'V' in Structure_20SCP.pdb V #2.22 to 'b'
Remapping chain ID 'W' in Structure_20SCP.pdb W #2.23 to 'c'
Remapping chain ID 'X' in Structure_20SCP.pdb X #2.24 to 'd'
Remapping chain ID 'Y' in Structure_20SCP.pdb Y #2.25 to 'e'
Remapping chain ID 'Z' in Structure_20SCP.pdb Z #2.26 to 'f'
Remapping chain ID 'a' in Structure_20SCP.pdb a #2.27 to 'g'
Remapping chain ID 'b' in Structure_20SCP.pdb b #2.28 to 'h'
> select add #3
113816 atoms, 115920 bonds, 28 pseudobonds, 14956 residues, 44 models selected
> select add #2
139546 atoms, 142096 bonds, 30 pseudobonds, 18272 residues, 61 models selected
> select subtract #2
91408 atoms, 93094 bonds, 28 pseudobonds, 12050 residues, 30 models selected
> select add #1
111298 atoms, 113334 bonds, 54 pseudobonds, 14752 residues, 57 models selected
> select subtract #1
56908 atoms, 57960 bonds, 14 pseudobonds, 7478 residues, 2 models selected
> hide #!2 models
> hide #!1 models
> select subtract #3
Nothing selected
> show #!7 models
> color zone #7 near #3 distance 11.3
> ui tool show "Side View"
> hide #!3 models
> rename #3 Structure_20SCP_preholo_docked_mature-beta-subunits
> select add #2
48138 atoms, 49002 bonds, 2 pseudobonds, 6222 residues, 31 models selected
> select add #1
102528 atoms, 104376 bonds, 42 pseudobonds, 13496 residues, 86 models selected
> select subtract #2
54390 atoms, 55374 bonds, 40 pseudobonds, 7274 residues, 55 models selected
> hide #!7 models
> show #!1 models
> show #!1.11 models
> show #!1.12 models
> show #1.13 models
> show #!1.14 models
> hide #!1.14 models
> show #!1.15 models
> show #!1.16 models
> show #!1.17 models
> show #!1.14 models
> hide #!1 models
> show #!1 models
> show #!1.28 models
> show #!1.29 models
> show #1.30 models
> show #!1.31 models
> show #!1.32 models
> hide #!1.32 models
> show #!1.33 models
> show #!1.34 models
> show #!1.32 models
> show #!2 models
> hide #!2 models
> combine sel
> show #!7 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 35 atomic
models, 1 maps.
> hide #!4 models
> show #!4 models
> hide #!1 models
> select subtract #1
Nothing selected
> color zone #7 near #4 distance 11.3
> show #!3 models
> hide #!4 models
> color zone #7 near #3 distance 11.3
> transparency 50
> rename #4 Structure_20SCP_preholo_mature_beta-subunits_docked
> rename #3 "Structure_20SCP_preholo_mature_beta-subunits_docked_split "
> hide #!3 models
> hide #!7 models
> show #!4 models
> save
> /Users/fadlof/Downloads/20SCP_preholo/Structure_20SCP_preholo_mature_beta-
> subunits_docking.pdb
> close #2
> rename #1 id #2
> rename #7 id #1
> show #!1 models
> show #!2 models
> transparency 0
> hide #!2 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!2 models
> show #!3 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!2 models
> show #!4 models
> select add #4
54390 atoms, 55374 bonds, 40 pseudobonds, 7274 residues, 2 models selected
[deleted to fit within tickets limits]
> rename #5 id #4
> 5
Unknown command: 5
> hide #!1 models
> hide #2.18 models
> hide #2.19 models
> hide #2.20 models
> hide #!2.21 models
> show #!2.21 models
> hide #2.22 models
> hide #2.23 models
> show #2.22 models
> hide #!2.21 models
> hide #2.24 models
> show #!2.21 models
> hide #!3 models
> hide #!2.21 models
> hide #2.22 models
> hide #2.25 models
> hide #!2.26 models
> hide #!2.27 models
> hide #!2.28 models
> hide #2.29 models
> hide #2.30 models
> hide #2.31 models
> hide #2.32 models
> hide #2.33 models
> hide #2.34 models
> show #!4 models
> select add #4
28800 atoms, 29331 bonds, 7 pseudobonds, 3780 residues, 22 models selected
> select subtract #4
Nothing selected
> select add #4
28800 atoms, 29331 bonds, 7 pseudobonds, 3780 residues, 22 models selected
> select subtract #4
Nothing selected
> select add #4
28800 atoms, 29331 bonds, 7 pseudobonds, 3780 residues, 22 models selected
> select subtract #4
Nothing selected
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> close #4
> close #6
> show #!1 models
> transparency 50
> hide #!1 models
> select #2/H:37-30
Nothing selected
> select #2/H:30-35
51 atoms, 51 bonds, 6 residues, 1 model selected
> show #!1 models
> select #2/H:30-34
40 atoms, 39 bonds, 5 residues, 1 model selected
> volume #1 level 0.08068
> volume #1 level 0.1043
> select #2/H:30-35
51 atoms, 51 bonds, 6 residues, 1 model selected
> view sel
> delete sel
> select #2/Y:30-35
51 atoms, 51 bonds, 6 residues, 1 model selected
> view sel
> view matrix models
> #2.25,1,-0.00024274,0.001022,0.074756,0.00024,1,0.002683,-0.28172,-0.0010227,-0.0026827,1,0.59998
> show #2.25 models
> delete sel
> hide #2.25 models
> hide #!2 models
> show #!2 models
> show #2.18 models
> show #2.19 models
> show #2.20 models
> show #!2.21 models
> show #2.22 models
> show #2.23 models
> show #2.25 models
> show #2.24 models
> show #!2.26 models
> show #2.34 models
> show #2.33 models
> show #2.32 models
> hide #2.32 models
> show #2.31 models
> show #2.30 models
> show #2.32 models
> show #2.29 models
> show #!2.28 models
> show #!2.27 models
> close #3
> view
> volume #1 level 0.07911
> volume #1 level 0.06967
> volume #1 level 0.01463
> volume #1 level 0.02
> volume #1 level 0.05
> select #2/V:243-247
35 atoms, 35 bonds, 5 residues, 1 model selected
> delete sel
> select #2/E:243-247
35 atoms, 35 bonds, 5 residues, 1 model selected
> view
> select up
112 atoms, 113 bonds, 14 residues, 1 model selected
> select up
1909 atoms, 1946 bonds, 247 residues, 1 model selected
> select #2/E:243-247
35 atoms, 35 bonds, 5 residues, 1 model selected
> delete sel
> volume #1 level 0.09718
> hide #!1 models
> select #2/C:236-238
27 atoms, 26 bonds, 3 residues, 1 model selected
> show #!1 models
> select #2/C:237-238
18 atoms, 17 bonds, 2 residues, 1 model selected
> delete sel
> select #2/T:237-238
18 atoms, 17 bonds, 2 residues, 1 model selected
> delete Sel
Missing or invalid "atoms" argument: invalid atoms specifier
> delete sel
> help help:user/tools/sideview.html
> volume #1 level 0.08774
> volume #1 level 0.06101
> select #2/U:128-129
13 atoms, 12 bonds, 2 residues, 1 model selected
> delete sel
> select #2/D:128-129
13 atoms, 12 bonds, 2 residues, 1 model selected
> delete sel
> volume #1 level 0.05315
> volume #1 level 0.04056
> select #2/L:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #2/c:2
12 atoms, 10 bonds, 2 residues, 2 models selected
> view sel
> hide #!1 models
> select #2/c:2
12 atoms, 10 bonds, 2 residues, 2 models selected
> view sel
> delete sel
> select add #2
57348 atoms, 58406 bonds, 14 pseudobonds, 7527 residues, 43 models selected
> hide #!2 models
> select subtract #2
Nothing selected
> show #!1 models
> combine #2
> color zone #1 near #3 distance 11.3
> view
> volume #1 level 0.08
> color zone #1 near #3 distance 11.3
> volume #1 level 0.095
> color zone #1 near #3 distance 11.3
> ui dockable false "Side View"
Window position QRect(1372,966 1188x266) outside any known screen, using
primary screen
> hide #!1 models
> select #3/H:3-28
Nothing selected
> select #3/b:3-28
186 atoms, 190 bonds, 26 residues, 1 model selected
> color red
> undo
> color sel orange
> select #3/H:3-28
Nothing selected
> color sel orange
> show #!1 models
> color zone #1 near #3 distance 11.3
> save "/Users/fadlof/Downloads/20SCP_preholo/Coot
> /Structure_20SCP_preholo_mature_beta-
> subunits_docked_real_space_refined_001-coot-1-1.pdb" models #3
> open "/Users/fadlof/Downloads/20SCP_preholo/Coot
> /Structure_20SCP_preholo_mature_beta-
> subunits_docked_real_space_refined_001-coot-1-1.pdb"
Chain information for Structure_20SCP_preholo_mature_beta-
subunits_docked_real_space_refined_001-coot-1-1.pdb #4
---
Chain | Description
A R | No description available
B S | No description available
C T | No description available
D U | No description available
E V | No description available
F W | No description available
G X | No description available
H Y | No description available
I Z | No description available
J a | No description available
K b | No description available
L c | No description available
M d | No description available
N e | No description available
O f | No description available
P g | No description available
Q h | No description available
> close #4
> rename #2 Structure_20SCP_preholo_mature_beta-
> subunits_docked_real_space_refined_001-coot-1-1.pdb
> save
> /Users/fadlof/Downloads/20SCP_preholo/ChimeraX_scessions/Structure_20SCP_preholo_model_building.cxs
> includeMaps true
——— End of log from Thu Sep 21 14:08:58 2023 ———
opened ChimeraX session
> rename #1 id #4
> rename #2 id #1
> rename #3 id #2
> rename #4 id #3
> color #1.8 #fe9000ff
> close #2
> color #1.9 #f4d1d1ff
> color #1.10 #d95728ff
> color #1.25 #fe9000ff
> color #1.26 #f4d1d1ff
> color #1.27 #d95728ff
> combine #1
> color zone #3 near #2 distance 11.3
> lighting soft
> open
> /Users/fadlof/Downloads/Maps_preholo20SCP/cryosparc_P109_J368_map_sharp.mrc
Opened cryosparc_P109_J368_map_sharp.mrc as #4, grid size 168,168,168, pixel
1.88, shown at level 0.119, step 1, values float32
> close #4
> save
> /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_preholo-20SCP/ChimeraX_scessions/Structure_20SCP_preholo_model_building.cxs
> includeMaps true
——— End of log from Mon Oct 2 19:49:22 2023 ———
opened ChimeraX session
> open
> /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_preholo-20SCP/Maps/cryosparc_P109_J413_map_sharp.mrc
Opened cryosparc_P109_J413_map_sharp.mrc as #4, grid size 168,168,168, pixel
1.88, shown at level 0.126, step 1, values float32
> open
> /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_preholo-20SCP/PDBs/Structure_20SCP_preholo_real_space_refined_002.pdb
Chain information for Structure_20SCP_preholo_real_space_refined_002.pdb #5
---
Chain | Description
A R | No description available
B S | No description available
C | No description available
D U | No description available
E V | No description available
F W | No description available
G X | No description available
H Y | No description available
I Z | No description available
J a | No description available
K b | No description available
L c | No description available
M d | No description available
N e | No description available
O f | No description available
P g | No description available
Q h | No description available
T | No description available
> style #!2,5 stick
Changed 114696 atom styles
> show #!2,5 cartoons
> hide #!2,5 cartoons
> show #!2,5 cartoons
> show #!2,5 atoms
> hide #!2,5 atoms
> show #!2,5 atoms
> hide #!2,5 atoms
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!4 models
> rename #5 Structure_20SCP_preholo.pdb
> select add #5
57348 atoms, 58406 bonds, 14 pseudobonds, 7527 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.86813,0.49629,-0.0071418,-56.488,-0.17851,0.32562,0.9285,-24.514,0.46313,-0.80478,0.37127,162.18
> view matrix models
> #5,0.78294,0.61669,0.081857,-77.362,0.48249,-0.68501,0.54587,96.626,0.3927,-0.38788,-0.83386,314.45
> view matrix models
> #5,0.82355,0.56686,0.020964,-65.435,0.56512,-0.81669,-0.11689,218.31,-0.049138,0.10811,-0.99292,333.22
> ui tool show "Fit in Map"
> fitmap #5 inMap #4
Fit molecule Structure_20SCP_preholo.pdb (#5) to map
cryosparc_P109_J413_map_sharp.mrc (#4) using 57348 atoms
average map value = 0.2695, steps = 80
shifted from previous position = 0.866
rotated from previous position = 8.2 degrees
atoms outside contour = 16986, contour level = 0.12615
Position of Structure_20SCP_preholo.pdb (#5) relative to
cryosparc_P109_J413_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.86564083 0.50066553 0.00006788 -58.01343851
0.50066553 -0.86564082 -0.00007881 216.20260911
0.00001930 0.00010221 -1.00000000 344.56156495
Axis 0.96582539 0.25919359 0.00001009
Axis point 0.00000000 115.87733080 172.28632961
Rotation angle (degrees) 179.99463081
Shift along axis 0.01095426
> select subtract #5
Nothing selected
> color zone #4 near #5 distance 11.3
> close #1
> close #2
> close #3
> split #5
Split Structure_20SCP_preholo.pdb (#5) into 34 models
Chain information for Structure_20SCP_preholo.pdb A #5.1
---
Chain | Description
A | No description available
Chain information for Structure_20SCP_preholo.pdb B #5.2
---
Chain | Description
B | No description available
Chain information for Structure_20SCP_preholo.pdb C #5.3
---
Chain | Description
C | No description available
Chain information for Structure_20SCP_preholo.pdb D #5.4
---
Chain | Description
D | No description available
Chain information for Structure_20SCP_preholo.pdb E #5.5
---
Chain | Description
E | No description available
Chain information for Structure_20SCP_preholo.pdb F #5.6
---
Chain | Description
F | No description available
Chain information for Structure_20SCP_preholo.pdb G #5.7
---
Chain | Description
G | No description available
Chain information for Structure_20SCP_preholo.pdb H #5.8
---
Chain | Description
H | No description available
Chain information for Structure_20SCP_preholo.pdb I #5.9
---
Chain | Description
I | No description available
Chain information for Structure_20SCP_preholo.pdb J #5.10
---
Chain | Description
J | No description available
Chain information for Structure_20SCP_preholo.pdb K #5.11
---
Chain | Description
K | No description available
Chain information for Structure_20SCP_preholo.pdb L #5.12
---
Chain | Description
L | No description available
Chain information for Structure_20SCP_preholo.pdb M #5.13
---
Chain | Description
M | No description available
Chain information for Structure_20SCP_preholo.pdb N #5.14
---
Chain | Description
N | No description available
Chain information for Structure_20SCP_preholo.pdb O #5.15
---
Chain | Description
O | No description available
Chain information for Structure_20SCP_preholo.pdb P #5.16
---
Chain | Description
P | No description available
Chain information for Structure_20SCP_preholo.pdb Q #5.17
---
Chain | Description
Q | No description available
Chain information for Structure_20SCP_preholo.pdb R #5.18
---
Chain | Description
R | No description available
Chain information for Structure_20SCP_preholo.pdb S #5.19
---
Chain | Description
S | No description available
Chain information for Structure_20SCP_preholo.pdb T #5.20
---
Chain | Description
T | No description available
Chain information for Structure_20SCP_preholo.pdb U #5.21
---
Chain | Description
U | No description available
Chain information for Structure_20SCP_preholo.pdb V #5.22
---
Chain | Description
V | No description available
Chain information for Structure_20SCP_preholo.pdb W #5.23
---
Chain | Description
W | No description available
Chain information for Structure_20SCP_preholo.pdb X #5.24
---
Chain | Description
X | No description available
Chain information for Structure_20SCP_preholo.pdb Y #5.25
---
Chain | Description
Y | No description available
Chain information for Structure_20SCP_preholo.pdb Z #5.26
---
Chain | Description
Z | No description available
Chain information for Structure_20SCP_preholo.pdb a #5.27
---
Chain | Description
a | No description available
Chain information for Structure_20SCP_preholo.pdb b #5.28
---
Chain | Description
b | No description available
Chain information for Structure_20SCP_preholo.pdb c #5.29
---
Chain | Description
c | No description available
Chain information for Structure_20SCP_preholo.pdb d #5.30
---
Chain | Description
d | No description available
Chain information for Structure_20SCP_preholo.pdb e #5.31
---
Chain | Description
e | No description available
Chain information for Structure_20SCP_preholo.pdb f #5.32
---
Chain | Description
f | No description available
Chain information for Structure_20SCP_preholo.pdb g #5.33
---
Chain | Description
g | No description available
Chain information for Structure_20SCP_preholo.pdb h #5.34
---
Chain | Description
h | No description available
> rename #4 id #1
> rename #5 id #3
> rename #3 id #2
> hide #!1 models
> color #2 #a3d1f6ff models
> color #2.2 #90c8f5ff
> hide #!2 models
> show #!2 models
> hide #2.1 models
> hide #2.2 models
> show #2.1 models
> show #2.2 models
> color #2 silver models
> color #2.1 #a3d1f6ff
> color #2.2 #90c8f5ff
> color #2.3 #59acefff
> color #2.4 #2590eaff
> color #2.5 #176fbbff
> color #2.6 #326cb1ff
> color #2.7 #c7e4faff
> color #2.8 #f4d5ffff
> color #2.9 #efc1ffff
> color #2.10 #e497ffff
> color #2.11 #d356ffff
> color #2.12 #c300ffff
> color #2.13 #a500e0ff
> color #2.14 #9600ccff
> color #2.15 #fe9000ff
> color #2.8 #fb6565ff
> color #2.8 #fe9000ff
> color #2.9 #fb6565ff
> color #2.10 #ffccccff
> color #2.11 #f4d5ffff
> color #2.12 #efc1ffff
> color #2.13 #e497ffff
> color #2.14 #d356ffff
> color #2.15 #c300ffff
> color #2.16 #a500e0ff
> color #2.17 #9600ccff
> color #2.18 #a3d1f6ff
> color #2.19 #90c8f5ff
> color #2.20 #59acefff
> color #2.21 #2590eaff
> color #2.22 #176fbbff
> color #2.23 #326cb1ff
> color #2.24 #fe9000ff
> color #2.24 #c7e4faff
> color #2.25 #fe9000ff
> color #2.26 #fb6565ff
> color #2.27 #ffccccff
> color #2.28 #f4d5ffff
> color #2.29 #efc1ffff
> color #2.29 #e497ffff
> color #2.29 #efc1ffff
> color #2.30 #e497ffff
> color #2.31 #d356ffff
> color #2.32 #c300ffff
> color #2.33 #a500e0ff
> color #2.34 #9600ccff
> combine #2
> rename #3 Structure_20SCP_preholo.pdb
> hide #!2 models
> show #!1 models
> color zone #1 near #3 distance 11.3
> ui tool show "Side View"
> color zone #1 near #3 distance 11.3
> save
> /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_preholo-20SCP/ChimeraX_scessions/Structure_20SCP_preholo_model_building.cxs
> includeMaps true
——— End of log from Wed Oct 4 16:50:44 2023 ———
opened ChimeraX session
> close #1
> rename #2 id #1
> rename #3 id #2
> open
> /Users/fadlof/Downloads/ModelBuilding/ModelBuilding_20SCP_preholo_v2/Phenix/RealSpaceRefine_1/Struture_20SCP_preholo_v2_real_space_refined_001.pdb
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb #3
---
Chain | Description
A R | No description available
B S | No description available
C | No description available
D U | No description available
E V | No description available
F W | No description available
G X | No description available
H Y | No description available
I Z | No description available
J a | No description available
K b | No description available
L c | No description available
M d | No description available
N e | No description available
O f | No description available
P g | No description available
Q h | No description available
T | No description available
> split #3
Split Struture_20SCP_preholo_v2_real_space_refined_001.pdb (#3) into 34 models
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb A
#3.1
---
Chain | Description
A | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb B
#3.2
---
Chain | Description
B | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb C
#3.3
---
Chain | Description
C | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb D
#3.4
---
Chain | Description
D | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb E
#3.5
---
Chain | Description
E | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb F
#3.6
---
Chain | Description
F | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb G
#3.7
---
Chain | Description
G | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb H
#3.8
---
Chain | Description
H | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb I
#3.9
---
Chain | Description
I | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb J
#3.10
---
Chain | Description
J | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb K
#3.11
---
Chain | Description
K | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb L
#3.12
---
Chain | Description
L | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb M
#3.13
---
Chain | Description
M | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb N
#3.14
---
Chain | Description
N | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb O
#3.15
---
Chain | Description
O | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb P
#3.16
---
Chain | Description
P | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb Q
#3.17
---
Chain | Description
Q | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb R
#3.18
---
Chain | Description
R | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb S
#3.19
---
Chain | Description
S | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb T
#3.20
---
Chain | Description
T | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb U
#3.21
---
Chain | Description
U | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb V
#3.22
---
Chain | Description
V | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb W
#3.23
---
Chain | Description
W | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb X
#3.24
---
Chain | Description
X | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb Y
#3.25
---
Chain | Description
Y | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb Z
#3.26
---
Chain | Description
Z | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb a
#3.27
---
Chain | Description
a | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb b
#3.28
---
Chain | Description
b | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb c
#3.29
---
Chain | Description
c | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb d
#3.30
---
Chain | Description
d | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb e
#3.31
---
Chain | Description
e | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb f
#3.32
---
Chain | Description
f | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb g
#3.33
---
Chain | Description
g | No description available
Chain information for Struture_20SCP_preholo_v2_real_space_refined_001.pdb h
#3.34
---
Chain | Description
h | No description available
> close #2
> close #1
> view
> style stick
Changed 57348 atom styles
> hide cartoons
> hide atoms
> show cartoons
> rename #3 id #1
> split #1
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb A, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb B, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb C, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb D, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb E, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb F, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb G, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb H, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb I, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb J, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb K, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb L, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb M, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb N, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb O, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb P, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb Q, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb R, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb S, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb T, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb U, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb V, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb W, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb X, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb Y, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb Z, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb a, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb b, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb c, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb d, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb e, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb f, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb g, has only
one piece
Did not split Struture_20SCP_preholo_v2_real_space_refined_001.pdb h, has only
one piece
> color #1.1 #a3d1f6ff
> color #1.2 #90c8f5ff
> color #1.3 #59acefff
> color #1.4 #2590eaff
> color #1.5 #176fbbff
> color #1.6 #326cb1ff
> color #1.7 #c7e4faff
> color #1.8 #fe9000ff
> color #1.9 #fb6565ff
> color #1.10 #ffccccff
> color #1.11 #f4d5ffff
> color #1.12 #efc1ffff
> color #1.13 #e497ffff
> color #1.14 #d356ffff
> color #1.15 #c300ffff
> color #1.16 #a500e0ff
> color #1.17 #9600ccff
> color #1.18 #a3d1f6ff
> color #1.19 #90c8f5ff
> color #1.20 #59acefff
> color #1.21 #2590eaff
> color #1.22 #176fbbff
> color #1.23 #326cb1ff
> color #1.24 #fe9000ff
> color #1.25 #fe9000ff
> color #1.25 #c7e4faff
> color #1.24 #c7e4faff
> color #1.25 #fe9000ff
> color #1.26 #fb6565ff
> color #1.27 #ffccccff
> color #1.28 #f4d5ffff
> color #1.29 #efc1ffff
> color #1.30 #e497ffff
> color #1.31 #d356ffff
> color #1.32 #c300ffff
> color #1.33 #a500e0ff
> color #1.34 #9600ccff
> select #2/K:1-43
Nothing selected
> color sel lime
> select #2/b:1-43
Nothing selected
> color sel lime
> ui tool show "Side View"
> select #3/K:1-43
Nothing selected
> color sel lime
> select #3/b:1-43
Nothing selected
> color sel lime
> select #1/K:1-43
216 atoms, 219 bonds, 1 pseudobond, 31 residues, 2 models selected
> color sel lime
> select #1/b:1-43
521 atoms, 529 bonds, 1 pseudobond, 72 residues, 3 models selected
> color sel lime
> select add #1
57348 atoms, 58406 bonds, 14 pseudobonds, 7527 residues, 43 models selected
> select subtract #1
Nothing selected
> hide #1.3 models
> select add #1.3
1744 atoms, 1767 bonds, 234 residues, 1 model selected
> select subtract #1.3
Nothing selected
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> hide #1.2 models
> show #1.2 models
> color #1.2 #fe9000ff
> color #1.2 #90c8f5ff
> open /Users/fadlof/Downloads/Manuscript/Structures/PDBs/Structure_20SCP.pdb
Chain information for Structure_20SCP.pdb #2
---
Chain | Description
A O | No description available
B P | No description available
C Q | No description available
D R | No description available
E S | No description available
F T | No description available
G U | No description available
H V | No description available
I W | No description available
J X | No description available
K Y | No description available
L Z | No description available
M a | No description available
N b | No description available
> show cartoons
> style stick
Changed 105288 atom styles
> hide cartoons
> show cartoons
> hide atoms
> show cartoons
> ui mousemode right "rotate selected models"
> select add #2
47940 atoms, 48784 bonds, 8 pseudobonds, 6174 residues, 2 models selected
> rename #1 Structure_20SCP_preholo_v2_real_space_refined_001.pdb
> rename #1 20SCP_preholo_v2_real_space_refined_001.pdb
> rename #2 20SCP.pdb
> view matrix models
> #2,-0.027297,-0.99954,0.01349,332.79,0.9996,-0.027201,0.0073078,3.3165,-0.0069375,0.013684,0.99988,-1.0954
> rename #2 id #3
> split #3
Split 20SCP.pdb (#3) into 28 models
Chain information for 20SCP.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for 20SCP.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for 20SCP.pdb C #3.3
---
Chain | Description
C | No description available
Chain information for 20SCP.pdb D #3.4
---
Chain | Description
D | No description available
Chain information for 20SCP.pdb E #3.5
---
Chain | Description
E | No description available
Chain information for 20SCP.pdb F #3.6
---
Chain | Description
F | No description available
Chain information for 20SCP.pdb G #3.7
---
Chain | Description
G | No description available
Chain information for 20SCP.pdb H #3.8
---
Chain | Description
H | No description available
Chain information for 20SCP.pdb I #3.9
---
Chain | Description
I | No description available
Chain information for 20SCP.pdb J #3.10
---
Chain | Description
J | No description available
Chain information for 20SCP.pdb K #3.11
---
Chain | Description
K | No description available
Chain information for 20SCP.pdb L #3.12
---
Chain | Description
L | No description available
Chain information for 20SCP.pdb M #3.13
---
Chain | Description
M | No description available
Chain information for 20SCP.pdb N #3.14
---
Chain | Description
N | No description available
Chain information for 20SCP.pdb O #3.15
---
Chain | Description
O | No description available
Chain information for 20SCP.pdb P #3.16
---
Chain | Description
P | No description available
Chain information for 20SCP.pdb Q #3.17
---
Chain | Description
Q | No description available
Chain information for 20SCP.pdb R #3.18
---
Chain | Description
R | No description available
Chain information for 20SCP.pdb S #3.19
---
Chain | Description
S | No description available
Chain information for 20SCP.pdb T #3.20
---
Chain | Description
T | No description available
Chain information for 20SCP.pdb U #3.21
---
Chain | Description
U | No description available
Chain information for 20SCP.pdb V #3.22
---
Chain | Description
V | No description available
Chain information for 20SCP.pdb W #3.23
---
Chain | Description
W | No description available
Chain information for 20SCP.pdb X #3.24
---
Chain | Description
X | No description available
Chain information for 20SCP.pdb Y #3.25
---
Chain | Description
Y | No description available
Chain information for 20SCP.pdb Z #3.26
---
Chain | Description
Z | No description available
Chain information for 20SCP.pdb a #3.27
---
Chain | Description
a | No description available
Chain information for 20SCP.pdb b #3.28
---
Chain | Description
b | No description available
> color #3.1 #a3d1f6ff
> color #3.2 #90c8f5ff
> color #3.3 #59acefff
> color #3.4 #2590eaff
> color #3.5 #176fbbff
> color #3.6 #326cb1ff
> color #3.7 #c7e4faff
> color #3.8 #f4d5ffff
> color #3.9 #efc1ffff
> color #3.10 #e497ffff
> color #3.11 #d356ffff
> color #3.12 #c300ffff
> color #3.13 #a500e0ff
> color #3.14 #9600ccff
> color #3.15 #a3d1f6ff
> color #3.16 #90c8f5ff
> color #3.17 #59acefff
> color #3.18 #2590eaff
> color #3.19 #176fbbff
> color #3.20 #326cb1ff
> color #3.21 #c7e4faff
> color #3.22 #f4d5ffff
> color #3.23 #efc1ffff
> color #3.24 #e497ffff
> color #3.25 #d356ffff
> color #3.26 #c300ffff
> color #3.27 #a500e0ff
> color #3.28 #9600ccff
> ui mousemode right "rotate selected models"
> select add #3
47940 atoms, 48784 bonds, 8 pseudobonds, 6174 residues, 37 models selected
> view matrix models
> #3,0.3497,0.86363,0.36312,-97.891,-0.82148,0.46901,-0.32435,279.82,-0.45042,-0.18487,0.87347,126.98
> view matrix models
> #3,-0.94214,0.33438,-0.023851,270.25,-0.17375,-0.54793,-0.81828,423.6,-0.28668,-0.76679,0.57433,246.68
> hide #!1 models
> select subtract #3
Nothing selected
> show #!1 models
> select add #1.2
1802 atoms, 1830 bonds, 248 residues, 1 model selected
> select subtract #1.2
Nothing selected
> select add #1.2
1802 atoms, 1830 bonds, 248 residues, 1 model selected
> select subtract #1.2
Nothing selected
> select add #3
47940 atoms, 48784 bonds, 8 pseudobonds, 6174 residues, 37 models selected
> view matrix models
> #3,-0.63882,-0.72459,-0.25861,437.65,0.58498,-0.23914,-0.77499,239.16,0.4997,-0.64636,0.57664,96.239
> view matrix models
> #3,0.80986,-0.56864,-0.14414,150.98,0.44664,0.757,-0.47693,45.999,0.38032,0.32187,0.86704,-94.143
> view matrix models
> #3,0.99008,-0.13218,0.047539,15.634,0.14035,0.94483,-0.29596,35.044,-0.0057951,0.2997,0.95402,-40.593
> view matrix models
> #3,0.99589,-0.090283,-0.007666,16.53,0.090061,0.99561,-0.02554,-11.349,0.0099381,0.024745,0.99964,-4.6038
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99589,-0.090283,-0.007666,11.89,0.090061,0.99561,-0.02554,-11.463,0.0099381,0.024745,0.99964,-3.2028
> view matrix models
> #3,0.99589,-0.090283,-0.007666,11.581,0.090061,0.99561,-0.02554,-12.786,0.0099381,0.024745,0.99964,-4.9988
> select subtract #3
Nothing selected
> open /Users/fadlof/Downloads/cryosparc_P109_J473_map_sharp.mrc
Opened cryosparc_P109_J473_map_sharp.mrc as #2, grid size 168,168,168, pixel
1.88, shown at level 0.126, step 1, values float32
> rename #2 id #4
> select add #3
47940 atoms, 48784 bonds, 8 pseudobonds, 6174 residues, 37 models selected
> select add #1
105288 atoms, 107190 bonds, 22 pseudobonds, 13701 residues, 80 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.72185,0.18933,0.66565,-99.897,0.68443,-0.052947,-0.72716,183.7,-0.10243,0.98048,-0.1678,65.061,#3,0.74255,0.1398,0.65504,-97.285,0.66962,-0.1325,-0.73079,195.94,-0.015371,0.98127,-0.192,52.177
> view matrix models
> #1,0.77513,0.51556,0.36521,-108.35,0.62805,-0.69162,-0.35666,229.88,0.068703,0.50583,-0.85989,234.2,#3,0.822,0.45235,0.34597,-107.79,0.55964,-0.75411,-0.34369,247.78,0.10543,0.47613,-0.87303,232.83
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.77513,0.51556,0.36521,-106.83,0.62805,-0.69162,-0.35666,220.96,0.068703,0.50583,-0.85989,201.33,#3,0.822,0.45235,0.34597,-106.27,0.55964,-0.75411,-0.34369,238.86,0.10543,0.47613,-0.87303,199.96
> view matrix models
> #1,0.77513,0.51556,0.36521,-105.3,0.62805,-0.69162,-0.35666,222.87,0.068703,0.50583,-0.85989,199.85,#3,0.822,0.45235,0.34597,-104.74,0.55964,-0.75411,-0.34369,240.77,0.10543,0.47613,-0.87303,198.47
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.71737,0.47193,0.51251,-115.15,0.69039,-0.58023,-0.43207,208.78,0.093462,0.66379,-0.74206,150.55,#3,0.76202,0.41777,0.49477,-115.44,0.631,-0.6507,-0.42239,226.36,0.14548,0.63407,-0.75946,146.86
> view matrix models
> #1,0.68906,0.48067,0.54236,-117.42,0.71754,-0.55748,-0.41755,198.5,0.10165,0.67689,-0.72904,144.96,#3,0.7349,0.42977,0.52461,-118.3,0.66023,-0.63015,-0.40867,216.03,0.15495,0.6467,-0.74684,141.13
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.76101,0.45099,0.46633,-110.53,0.64754,-0.57177,-0.50376,226.46,0.039442,0.68534,-0.72716,152.82,#3,0.80313,0.39184,0.44881,-109.81,0.58837,-0.64019,-0.49394,243.79,0.093776,0.66077,-0.74471,148.15
> view matrix models
> #1,0.64946,0.52771,0.54747,-119.69,0.75854,-0.49985,-0.41804,183.06,0.05305,0.68678,-0.72492,150.11,#3,0.69975,0.4803,0.52882,-121.66,0.70625,-0.57648,-0.41094,200.32,0.10748,0.66104,-0.74261,145.56
> view matrix models
> #1,0.68943,0.58571,0.42618,-113.93,0.70321,-0.40009,-0.58773,205.16,-0.17373,0.70489,-0.68771,175.39,#3,0.74358,0.53144,0.40578,-115.57,0.65844,-0.47637,-0.58269,221.35,-0.11636,0.70046,-0.70414,167.8
> view matrix models
> #1,0.61113,0.54059,0.57817,-121.29,0.78845,-0.48017,-0.38443,169.39,0.069798,0.6908,-0.71967,145.97,#3,0.66305,0.49735,0.55947,-124.02,0.73814,-0.55876,-0.37808,186.58,0.12457,0.66365,-0.7376,141.54
> view matrix models
> #1,0.63251,0.5509,0.54446,-120.52,0.77455,-0.4473,-0.44721,177.03,-0.002833,0.70457,-0.70962,153.19,#3,0.68493,0.50485,0.52535,-122.96,0.72663,-0.52633,-0.44157,193.95,0.053581,0.68418,-0.72735,147.69
> view matrix models
> #1,0.59051,0.62886,0.5058,-120.24,0.80215,-0.52621,-0.28224,156.64,0.088665,0.57239,-0.81517,178.39,#3,0.64974,0.5853,0.48503,-123.97,0.74865,-0.60331,-0.27485,174.07,0.13175,0.5417,-0.83018,176.17
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.59051,0.62886,0.5058,-127.18,0.80215,-0.52621,-0.28224,166.79,0.088665,0.57239,-0.81517,176.58,#3,0.64974,0.5853,0.48503,-130.91,0.74865,-0.60331,-0.27485,184.22,0.13175,0.5417,-0.83018,174.37
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.6535,0.55296,0.51689,-127.25,0.7439,-0.59531,-0.30366,191.69,0.1398,0.58296,-0.80039,164.52,#3,0.70575,0.50432,0.49757,-129.33,0.68421,-0.66738,-0.29405,209.43,0.18378,0.54797,-0.81606,162.69
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.6535,0.55296,0.51689,-122.79,0.7439,-0.59531,-0.30366,190.63,0.1398,0.58296,-0.80039,166.16,#3,0.70575,0.50432,0.49757,-124.88,0.68421,-0.66738,-0.29405,208.37,0.18378,0.54797,-0.81606,164.32
> ui tool show "Fit in Map"
> fitmap #1.1 inMap #4
Fit molecule Struture_20SCP_preholo_v2_real_space_refined_001.pdb A (#1.1) to
map cryosparc_P109_J473_map_sharp.mrc (#4) using 1720 atoms
average map value = 0.1297, steps = 212
shifted from previous position = 17.7
rotated from previous position = 16.4 degrees
atoms outside contour = 1124, contour level = 0.12571
Position of Struture_20SCP_preholo_v2_real_space_refined_001.pdb A (#1.1)
relative to cryosparc_P109_J473_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.98563238 -0.02790418 -0.16658383 40.62428330
0.06539518 0.97238256 0.22404379 -52.72813305
0.15573146 -0.23171859 0.96023654 23.80870138
Axis -0.80529012 -0.56950141 0.16485137
Axis point 0.00000000 60.73630497 239.68406271
Rotation angle (degrees) 16.43815564
Shift along axis 1.23930918
> undo
> combine #1
> close #2
> combine #1
> combine #3
> rename #2 20SCP_preholo_v2_real_space_refined_001.pdb
> rename #5 20SCP.pdb
> rename #4 id #6
> rename #6 id #4
> rename #4 id #6
> rename #5 id #4
> rename #6 id #7
> rename #4 id #6
> rename #3 id #5
> close #1
> select subtract #5
Nothing selected
> close #5
> hide #!6 models
> fitmap #2 inMap #7
Fit molecule 20SCP_preholo_v2_real_space_refined_001.pdb (#2) to map
cryosparc_P109_J473_map_sharp.mrc (#7) using 57348 atoms
average map value = 0.262, steps = 204
shifted from previous position = 6.95
rotated from previous position = 31.2 degrees
atoms outside contour = 17464, contour level = 0.12571
Position of 20SCP_preholo_v2_real_space_refined_001.pdb (#2) relative to
cryosparc_P109_J473_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.80676916 0.59074841 0.01182635 -66.05750055
0.57000381 -0.77285526 -0.27890933 248.20605753
-0.15562519 0.23175651 -0.96024462 292.45896567
Axis 0.94951134 0.31135259 -0.03857166
Axis point 0.00000000 113.82906765 162.71743593
Rotation angle (degrees) 164.40059527
Shift along axis 3.27662520
> show #!6 models
> hide #!2 models
> fitmap #6 inMap #7
Fit molecule 20SCP.pdb (#6) to map cryosparc_P109_J473_map_sharp.mrc (#7)
using 47940 atoms
average map value = 0.2055, steps = 112
shifted from previous position = 4.31
rotated from previous position = 17.2 degrees
atoms outside contour = 21600, contour level = 0.12571
Position of 20SCP.pdb (#6) relative to cryosparc_P109_J473_map_sharp.mrc (#7)
coordinates:
Matrix rotation and translation
0.29509812 -0.74954326 0.59253860 131.60198787
-0.58433684 -0.63223828 -0.50874867 447.08612476
0.75595472 -0.19611136 -0.62455807 156.05278266
Axis 0.80258429 -0.41951234 0.42410830
Axis point -0.00000000 247.96895511 70.23713595
Rotation angle (degrees) 168.76876190
Shift along axis -15.75317566
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5rc202211182308 (2022-11-18)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.2.44
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2,7 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0)
OS Loader Version: 564.40.4~27
Software:
System Software Overview:
System Version: macOS 13.0.1 (22A400)
Kernel Version: Darwin 22.1.0
Time since boot: 6 Tage, 6 Stunden und 27 Minuten
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5rc202211182308
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.3
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.0.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.0.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.32
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.1
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.12
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.10.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 655 |
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Apple Intel graphics driver crash.