Opened 3 years ago

Closed 3 years ago

#8777 closed defect (nonchimerax)

Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x00007ff8558fe680 (most recent call first):
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2730 in draw_elements
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1736 in draw
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 836 in _draw_geometry
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 771 in draw_self
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 764 in draw
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1551 in _draw_multiple
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1538 in draw_opaque
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 247 in _draw_scene
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 177 in draw
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.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 "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 158 in update_graphics_now
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/graphics.py", line 145 in resizeEvent
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/graphics.py", line 57 in event
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.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":"2023-04-03 21:12:52.00 -0400","app_version":"1.5.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.2.1 (22D68)","roots_installed":0,"name":"ChimeraX","incident_id":"7E5F8FD2-813A-47EE-9112-E332DD76BDE4"}
{
  "uptime" : 120000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,2",
  "coalitionID" : 1127,
  "osVersion" : {
    "train" : "macOS 13.2.1",
    "build" : "22D68",
    "releaseType" : "User"
  },
  "captureTime" : "2023-04-03 21:12:44.8102 -0400",
  "incident" : "7E5F8FD2-813A-47EE-9112-E332DD76BDE4",
  "pid" : 48056,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-04-03 20:53:32.3836 -0400",
  "procStartAbsTime" : 119889356975325,
  "procExitAbsTime" : 121041888319341,
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"7E9E0758-4285-5816-A1F0-9E5A6876999A","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "A1D4F363-6D00-BDAF-80F4-3DDF79D90485",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 30653,
  "bridgeVersion" : {"build":"20P3045","train":"7.2"},
  "sleepWakeUUID" : "F0186B0E-C0F9-421A-BAD0-9587CE4DF65C",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\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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===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/dingyongbo/Downloads/cryosparc_P3_J290_005_volume_map_sharp.mrc

Opened cryosparc_P3_J290_005_volume_map_sharp.mrc as #1, grid size
224,224,224, pixel 0.825, shown at level 0.0448, step 1, values float32  

> open /Users/dingyongbo/Downloads/cryosparc_P3_J288_005_volume_map_sharp.mrc

Opened cryosparc_P3_J288_005_volume_map_sharp.mrc as #2, grid size
112,112,112, pixel 1.65, shown at level 0.127, step 1, values float32  

> tile columns 3 spacingFactor 0.6

2 models tiled  

> volume #2 level 0.2095

> volume #1 level 0.07867

> ui mousemode right zoom

> volume #2 level 0.202

> tile columns 3 spacingFactor 0.8

2 models tiled  

> open /Users/dingyongbo/Downloads/cryosparc_P3_J301_005_volume_map_sharp.mrc

Opened cryosparc_P3_J301_005_volume_map_sharp.mrc as #3, grid size
224,224,224, pixel 0.825, shown at level 0.0442, step 1, values float32  

> tile columns 3 spacingFactor 0.8

3 models tiled  

> volume #3 level 0.07665

> select add #3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.10656,-0.12312,-0.98665,373.07,0.80081,-0.59881,-0.011765,89.136,-0.58937,-0.79137,0.1624,195.51

> view matrix models
> #3,-0.03392,-0.0079143,-0.99939,357.82,0.40569,-0.91399,-0.0065317,148.17,-0.91338,-0.40567,0.034214,194.43

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.03392,-0.0079143,-0.99939,388.59,0.40569,-0.91399,-0.0065317,131.5,-0.91338,-0.40567,0.034214,194.43

> select subtract #3

Nothing selected  

> ui mousemode right zoom

> select add #3

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.0024684,0.15393,-0.98808,372.92,-0.87731,-0.47453,-0.071735,233.01,-0.47992,0.86667,0.13622,32.012

> view matrix models
> #3,0.98178,-0.18999,0.0041723,206.48,-0.088558,-0.43797,0.89461,64.752,-0.16814,-0.87868,-0.44682,226.37

> view matrix models
> #3,0.98555,0.16303,0.045887,162.11,-0.16833,0.97286,0.15879,8.1128,-0.018754,-0.16422,0.98625,20.145

> view matrix models
> #3,0.75394,-0.60993,-0.24404,275.75,0.64939,0.63579,0.41721,-70.762,-0.099312,-0.47303,0.87543,65.357

> view matrix models
> #3,0.9203,-0.27287,-0.28033,237.11,0.2695,-0.077199,0.9599,-6.8803,-0.28357,-0.95895,0.0024905,202.77

> view matrix models
> #3,0.93999,-0.064538,-0.33504,217.3,0.22914,0.84697,0.47973,-57.342,0.25281,-0.52771,0.81093,49.959

> tile columns 3 spacingFactor 0.8

3 models tiled  

> view matrix models
> #3,0.8617,0.45592,-0.22274,131.95,0.0082645,0.4263,0.90455,-27.146,0.50735,-0.78129,0.36357,99.271

> view matrix models
> #3,0.90071,0.40026,-0.16887,128.3,-0.26833,0.81829,0.50833,-1.8162,0.34165,-0.41255,0.84444,33.938

> select subtract #3

Nothing selected  

> ui mousemode right zoom

> tile columns 3 spacingFactor 1

3 models tiled  

> select add #3

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.013488,-0.13326,0.99099,218.64,-0.86364,0.50104,0.055619,127.1,-0.50393,-0.85511,-0.12184,224.94

> select subtract #3

Nothing selected  

> ui mousemode right zoom

> hide #!2 models

> tile columns 3 spacingFactor 1

2 models tiled  

> save /Users/dingyongbo/Desktop/ChimeraX/SisAgo-Aga1/sgRNA_Compare.cxs

> open /Users/dingyongbo/Desktop/ChimeraX/SisAgo-Aga1/docking_0403.cxs

Opened cryosparc_P3_J291_class_00_00063_volume.mrc as #1, grid size 72,72,72,
pixel 2.57, shown at level 0.148, step 1, values float32  
Opened cryosparc_P3_J283_006_volume_map_sharp.mrc as #9, grid size
112,112,112, pixel 1.65, shown at level 0.128, step 1, values float32  
Opened cryosparc_P3_J299_007_volume_map_sharp.mrc as #14, grid size
224,224,224, pixel 0.825, shown at level 0.0418, step 1, values float32  
Opened cryosparc_P3_J299_007_volume_mask_refine.mrc as #15, grid size
224,224,224, pixel 0.825, shown at level 0.99, step 1, values float32  
Opened cryosparc_P3_J300_005_volume_mask_refine.mrc as #16, grid size
224,224,224, pixel 0.825, shown at level 1, step 1, values float32  
Opened cryosparc_P3_J300_005_volume_map_sharp.mrc as #17, grid size
224,224,224, pixel 0.825, shown at level 0.0344, step 1, values float32  
opened ChimeraX session  

> hide #12 models

> open /Users/dingyongbo/Desktop/ChimeraX/SisAgo-
> Aga1/AgoAga1_dock_0403/Aga1.pdb

Chain information for Aga1.pdb #2  
---  
Chain | Description  
B | No description available  
  

> open "/Users/dingyongbo/Desktop/Profile in Ke Lab/Project/Aga2/Structural
> Prediction/SisAga1_prediction_1/best_model.pdb"

Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #3 models

> show #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> close #2

> open "/Users/dingyongbo/Desktop/Profile in Ke Lab/Project/Aga2/Structural
> Prediction/SisAgo.pdb"

Chain information for SisAgo.pdb #2  
---  
Chain | Description  
C | No description available  
  

> tile columns 3 spacingFactor 1

3 models tiled  

> select add #2

3722 atoms, 3806 bonds, 459 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.93629,-0.35086,-0.016096,103.69,0.34752,0.9188,0.18718,30.812,-0.050886,-0.18085,0.98219,172.29

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.45875,-0.56927,-0.68226,102.26,-0.84504,-0.51688,-0.13693,28.595,-0.2747,0.63935,-0.71817,170.2

> view matrix models
> #2,0.85351,-0.34328,0.39202,105.21,-0.39891,-0.91448,0.067724,26.755,0.33524,-0.21418,-0.91746,165.22

> view matrix models
> #2,0.66671,0.68504,0.29361,108.64,-0.17086,-0.24298,0.95487,30.985,0.72547,-0.68679,-0.044953,165.38

> view matrix models
> #2,0.44382,0.88498,-0.1408,108.53,-0.83661,0.46551,0.28877,32.97,0.3211,-0.010374,0.94699,171.69

> view matrix models
> #2,0.51167,0.14816,-0.84631,103.85,-0.85374,-0.023016,-0.52019,28.976,-0.09655,0.9887,0.11471,173.39

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.51167,0.14816,-0.84631,84.528,-0.85374,-0.023016,-0.52019,79.287,-0.09655,0.9887,0.11471,74.775

> view matrix models
> #2,0.77707,-0.21283,-0.59234,85.286,-0.62601,-0.35913,-0.6922,75.806,-0.06541,0.90869,-0.41231,72.478

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 104  
shifted from previous position = 1.9  
rotated from previous position = 38.9 degrees  
atoms outside contour = 2172, contour level = 0.14802  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28400201 0.60577398 -0.74322335 93.48201821  
0.80409646 -0.27174838 -0.52875506 93.49394248  
-0.52227573 -0.74779066 -0.40992357 97.97109234  
Axis -0.59366818 -0.59885045 0.53752789  
Axis point -9.66794343 0.00000000 95.49451496  
Rotation angle (degrees) 169.36939025  
Shift along axis -58.82399494  
  

> select subtract #2

Nothing selected  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 60  
shifted from previous position = 5.87  
rotated from previous position = 0.019 degrees  
atoms outside contour = 2170, contour level = 0.14802  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28412621 0.60551588 -0.74338618 93.48088556  
0.80409617 -0.27180586 -0.52872595 93.49483757  
-0.52220861 -0.74797878 -0.40966578 97.97137791  
Axis -0.59360495 -0.59881597 0.53763612  
Axis point -9.67819644 0.00000000 95.51239664  
Rotation angle (degrees) 169.35757770  
Shift along axis -58.80396710  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 56  
shifted from previous position = 0.00498  
rotated from previous position = 0.0552 degrees  
atoms outside contour = 2172, contour level = 0.14802  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28363924 0.60620423 -0.74301104 93.48397202  
0.80424245 -0.27160274 -0.52860783 93.49848886  
-0.52224807 -0.74749485 -0.41049793 97.97471878  
Axis -0.59383131 -0.59892068 0.53726939  
Axis point -9.66672790 0.00000000 95.46547348  
Rotation angle (degrees) 169.37963769  
Shift along axis -58.87307092  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 60  
shifted from previous position = 0.0412  
rotated from previous position = 0.0451 degrees  
atoms outside contour = 2173, contour level = 0.14802  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28408730 0.60565620 -0.74328674 93.46337618  
0.80411682 -0.27171612 -0.52874067 93.53462647  
-0.52219799 -0.74789778 -0.40982718 97.96877344  
Axis -0.59362599 -0.59885818 0.53756587  
Axis point -9.70012835 0.00000000 95.51527022  
Rotation angle (degrees) 169.36265966  
Shift along axis -58.83159604  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 44  
shifted from previous position = 0.0473  
rotated from previous position = 0.01 degrees  
atoms outside contour = 2169, contour level = 0.14802  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28396655 0.60568645 -0.74330823 93.48294349  
0.80408184 -0.27186768 -0.52871595 93.49080711  
-0.52231750 -0.74781820 -0.40982010 97.97180107  
Axis -0.59368054 -0.59879756 0.53757315  
Axis point -9.67462421 0.00000000 95.50288900  
Rotation angle (degrees) 169.36634217  
Shift along axis -58.81406225  
  

> select add #3

2047 atoms, 2080 bonds, 243 residues, 1 model selected  

> view matrix models
> #3,0.91167,-0.4095,0.034264,139.28,0.37681,0.79979,-0.46727,7.5823,0.16394,0.43891,0.88345,137.79

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.30221,-0.84852,0.43437,143.39,0.45603,-0.27146,-0.84755,9.9241,0.83708,0.45422,0.30492,134.44

> view matrix models
> #3,0.13176,-0.96957,0.20634,145.06,0.066182,-0.19909,-0.97774,12.398,0.98907,0.14249,0.037936,134.56

> view matrix models
> #3,-0.57356,-0.78122,-0.24642,149.74,-0.62852,0.61261,-0.47923,14.256,0.52534,-0.11999,-0.84239,139.34

> view matrix models
> #3,-0.76881,0.62592,0.13098,147.42,0.47354,0.41959,0.77441,5.8896,0.42976,0.65739,-0.61898,137.96

> view matrix models
> #3,-0.7597,-0.61576,0.20905,149.86,-0.29251,0.036472,-0.95557,14.102,0.58077,-0.78709,-0.20782,139.43

> view matrix models
> #3,-0.72583,0.52773,0.44121,146.89,0.18979,0.77015,-0.60897,9.0253,-0.66117,-0.35827,-0.65916,146.95

> view matrix models
> #3,-0.76534,0.59862,0.23644,147.3,0.21685,0.58572,-0.78097,9.5071,-0.60599,-0.54643,-0.57809,146.88

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.76534,0.59862,0.23644,98.232,0.21685,0.58572,-0.78097,63.49,-0.60599,-0.54643,-0.57809,100.22

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 120  
shifted from previous position = 1.91  
rotated from previous position = 35.8 degrees  
atoms outside contour = 1145, contour level = 0.14802  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03034396 0.12474393 -0.99172496 96.32008403  
-0.55611859 0.82232818 0.12045204 92.30113170  
0.83054894 0.55517160 0.04441972 66.53207024  
Axis 0.21809060 -0.91420042 -0.34157588  
Axis point 40.46471607 0.00000000 74.01783242  
Rotation angle (degrees) 94.69192351  
Shift along axis -86.10097881  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.0514  
rotated from previous position = 0.0792 degrees  
atoms outside contour = 1139, contour level = 0.14802  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03147066 0.12428715 -0.99174720 96.30093637  
-0.55556539 0.82266178 0.12072662 92.31593752  
0.83087717 0.55477969 0.04315993 66.57420079  
Axis 0.21777476 -0.91445403 -0.34109820  
Axis point 40.42980841 0.00000000 73.97166611  
Rotation angle (degrees) 94.75093488  
Shift along axis -86.15510832  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.00873  
rotated from previous position = 0.0324 degrees  
atoms outside contour = 1140, contour level = 0.14802  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03091135 0.12421481 -0.99177386 96.30411460  
-0.55554957 0.82272652 0.12035769 92.31446558  
0.83090874 0.55469988 0.04357589 66.56710280  
Axis 0.21791040 -0.91444371 -0.34103923  
Axis point 40.42535086 0.00000000 74.00717777  
Rotation angle (degrees) 94.72103897  
Shift along axis -86.13270789  
  

> select subtract #3

Nothing selected  

> ui mousemode right zoom

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 52  
shifted from previous position = 1.95  
rotated from previous position = 0.0603 degrees  
atoms outside contour = 1148, contour level = 0.14802  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03026880 0.12474466 -0.99172717 96.32323800  
-0.55608092 0.82235938 0.12041300 92.29775611  
0.83057691 0.55512523 0.04447629 66.51685765  
Axis 0.21808546 -0.91420943 -0.34155505  
Axis point 40.46938096 0.00000000 74.01663685  
Rotation angle (degrees) 94.68724036  
Shift along axis -86.09195021  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 36  
shifted from previous position = 0.0551  
rotated from previous position = 0.0436 degrees  
atoms outside contour = 1141, contour level = 0.14802  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03088814 0.12517885 -0.99165336 96.30076219  
-0.55604695 0.82227879 0.12111810 92.31928918  
0.83057684 0.55514687 0.04420665 66.56194635  
Axis 0.21775129 -0.91420894 -0.34176951  
Axis point 40.45442142 0.00000000 73.97971727  
Rotation angle (degrees) 94.71511001  
Shift along axis -86.17834763  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 60  
shifted from previous position = 0.041  
rotated from previous position = 0.0703 degrees  
atoms outside contour = 1141, contour level = 0.14802  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03091934 0.12411592 -0.99178599 96.32718411  
-0.55557788 0.82271897 0.12027859 92.29326547  
0.83088952 0.55473322 0.04351812 66.53880821  
Axis 0.21796747 -0.91444293 -0.34100485  
Axis point 40.44348164 0.00000000 74.00610448  
Rotation angle (degrees) 94.72314618  
Shift along axis -86.09078845  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 48  
shifted from previous position = 0.0215  
rotated from previous position = 0.0781 degrees  
atoms outside contour = 1147, contour level = 0.14802  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03012875 0.12484847 -0.99171837 96.32431088  
-0.55626317 0.82223630 0.12041166 92.29857214  
0.83045995 0.55528418 0.04467565 66.51862786  
Axis 0.21816393 -0.91413821 -0.34169552  
Axis point 40.47591112 0.00000000 74.02331174  
Rotation angle (degrees) 94.68102233  
Shift along axis -86.08827869  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 36  
shifted from previous position = 0.0527  
rotated from previous position = 0.0511 degrees  
atoms outside contour = 1141, contour level = 0.14802  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03090425 0.12521443 -0.99164837 96.30211389  
-0.55604425 0.82227494 0.12115667 92.31812837  
0.83057805 0.55514455 0.04421297 66.56121462  
Axis 0.21773090 -0.91420755 -0.34178619  
Axis point 40.45536992 0.00000000 73.97833226  
Rotation angle (degrees) 94.71550223  
Shift along axis -86.17968845  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 60  
shifted from previous position = 0.0444  
rotated from previous position = 0.0366 degrees  
atoms outside contour = 1145, contour level = 0.14802  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03040462 0.12483764 -0.99171132 96.32280480  
-0.55615262 0.82228912 0.12056154 92.29439711  
0.83052393 0.55520840 0.04442739 66.53024273  
Axis 0.21805495 -0.91418450 -0.34164125  
Axis point 40.46778075 0.00000000 74.01260719  
Rotation angle (degrees) 94.69456951  
Shift along axis -86.09991763  
  

> volume #1 level 0.1818

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 60  
shifted from previous position = 0.00867  
rotated from previous position = 0.00355 degrees  
atoms outside contour = 1405, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03044689 0.12481011 -0.99171348 96.31967382  
-0.55612281 0.82230896 0.12056373 92.30115537  
0.83054235 0.55518520 0.04437299 66.53438976  
Axis 0.21804291 -0.91419771 -0.34161357  
Axis point 40.46547457 0.00000000 74.01085212  
Rotation angle (degrees) 94.69677781  
Shift along axis -86.10873389  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 48  
shifted from previous position = 0.019  
rotated from previous position = 0.0318 degrees  
atoms outside contour = 1407, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.02989607 0.12474754 -0.99173811 96.32579565  
-0.55612275 0.82236129 0.12020656 92.29597037  
0.83056240 0.55512175 0.04478957 66.51795423  
Axis 0.21818112 -0.91418183 -0.34156784  
Axis point 40.46637714 0.00000000 74.04223242  
Rotation angle (degrees) 94.66746684  
Shift along axis -86.07922291  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 40  
shifted from previous position = 0.0434  
rotated from previous position = 0.0725 degrees  
atoms outside contour = 1407, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03092581 0.12501259 -0.99167316 96.31937975  
-0.55666630 0.82188171 0.12096820 92.29110726  
0.83016047 0.55577200 0.04417294 66.55917110  
Axis 0.21814435 -0.91402772 -0.34200346  
Axis point 40.48263271 0.00000000 73.98495774  
Rotation angle (degrees) 94.72857650  
Shift along axis -86.10856836  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 40  
shifted from previous position = 0.0254  
rotated from previous position = 0.0331 degrees  
atoms outside contour = 1407, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03081906 0.12483506 -0.99169885 96.32007201  
-0.55622600 0.82220666 0.12078523 92.30216456  
0.83045951 0.55533109 0.04409686 66.53710687  
Axis 0.21801173 -0.91417716 -0.34168845  
Axis point 40.47434283 0.00000000 73.98696111  
Rotation angle (degrees) 94.71835384  
Shift along axis -86.11658614  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 48  
shifted from previous position = 0.0371  
rotated from previous position = 0.0678 degrees  
atoms outside contour = 1405, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03084428 0.12415442 -0.99178351 96.30416353  
-0.55544174 0.82281125 0.12027610 92.31436989  
0.83098333 0.55458771 0.04358152 66.56594749  
Axis 0.21789363 -0.91448001 -0.34095261  
Axis point 40.41994322 0.00000000 74.01312137  
Rotation angle (degrees) 94.71651312  
Shift along axis -86.13141537  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.00718  
rotated from previous position = 0.0195 degrees  
atoms outside contour = 1405, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03112604 0.12426149 -0.99176129 96.30205885  
-0.55556301 0.82269447 0.12051461 92.31585861  
0.83089174 0.55473696 0.04342786 66.57242477  
Axis 0.21785384 -0.91444386 -0.34107498  
Axis point 40.42618061 -0.00000000 73.99401579  
Rotation angle (degrees) 94.73238660  
Shift along axis -86.14408463  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.00345  
rotated from previous position = 0.00849 degrees  
atoms outside contour = 1406, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03098418 0.12422201 -0.99177068 96.30323341  
-0.55555574 0.82271562 0.12040367 92.31511825  
0.83090191 0.55471443 0.04352107 66.56944203  
Axis 0.21789588 -0.91444394 -0.34104789  
Axis point 40.42537610 0.00000000 74.00305735  
Rotation angle (degrees) 94.72502128  
Shift along axis -86.13629092  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.00234  
rotated from previous position = 0.00478 degrees  
atoms outside contour = 1405, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03106601 0.12423713 -0.99176623 96.30245936  
-0.55555725 0.82270614 0.12046145 92.31563255  
0.83089784 0.55472510 0.04346263 66.57148290  
Axis 0.21787360 -0.91444535 -0.34105836  
Axis point 40.42551502 -0.00000000 73.99814036  
Rotation angle (degrees) 94.72932598  
Shift along axis -86.14059811  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 48  
shifted from previous position = 1.2  
rotated from previous position = 0.055 degrees  
atoms outside contour = 2589, contour level = 0.1818  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28456287 0.60558376 -0.74316383 93.45934088  
0.80431278 -0.27100185 -0.52880919 93.54855022  
-0.52163696 -0.74821553 -0.40996164 97.96417915  
Axis -0.59340959 -0.59914481 0.53748541  
Axis point -9.68077486 0.00000000 95.49724955  
Rotation angle (degrees) 169.34649252  
Shift along axis -58.85448039  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 48  
shifted from previous position = 0.00392  
rotated from previous position = 0.0655 degrees  
atoms outside contour = 2590, contour level = 0.1818  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28409377 0.60550306 -0.74340902 93.45612538  
0.80393542 -0.27207820 -0.52883031 93.54565869  
-0.52247369 -0.74789014 -0.40948959 97.96928578  
Axis -0.59362750 -0.59870988 0.53772937  
Axis point -9.71837129 0.00000000 95.54341878  
Rotation angle (degrees) 169.36746374  
Shift along axis -58.80387376  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 44  
shifted from previous position = 0.0623  
rotated from previous position = 0.0262 degrees  
atoms outside contour = 2597, contour level = 0.1818  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28385514 0.60578501 -0.74327046 93.48370305  
0.80406828 -0.27193044 -0.52870431 93.49026184  
-0.52239894 -0.74771554 -0.40990360 97.97163795  
Axis -0.59373266 -0.59877584 0.53753979  
Axis point -9.67503261 0.00000000 95.49884568  
Rotation angle (degrees) 169.37175459  
Shift along axis -58.82038312  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 44  
shifted from previous position = 0.0595  
rotated from previous position = 0.0265 degrees  
atoms outside contour = 2591, contour level = 0.1818  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28415449 0.60547007 -0.74341268 93.45771539  
0.80400623 -0.27193843 -0.52879454 93.54414748  
-0.52233168 -0.74796768 -0.40952913 97.96536741  
Axis -0.59359627 -0.59876341 0.53770424  
Axis point -9.71504073 0.00000000 95.53725117  
Rotation angle (degrees) 169.36133405  
Shift along axis -58.81057026  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 44  
shifted from previous position = 0.059  
rotated from previous position = 0.0254 degrees  
atoms outside contour = 2597, contour level = 0.1818  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28386637 0.60576994 -0.74327845 93.48329051  
0.80406861 -0.27192925 -0.52870442 93.49086076  
-0.52239233 -0.74772818 -0.40988897 97.97244855  
Axis -0.59372725 -0.59877572 0.53754589  
Axis point -9.67583480 0.00000000 95.50037031  
Rotation angle (degrees) 169.37104182  
Shift along axis -58.81894804  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 72  
shifted from previous position = 6.31  
rotated from previous position = 0.054 degrees  
atoms outside contour = 1404, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03062542 0.12477300 -0.99171266 96.29758495  
-0.55607889 0.82232832 0.12063426 92.32080113  
0.83056519 0.55516487 0.04419948 66.56267412  
Axis 0.21800032 -0.91422131 -0.34157761  
Axis point 40.44839524 0.00000000 74.00339199  
Rotation angle (degrees) 94.70634104  
Shift along axis -86.14505866  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 60  
shifted from previous position = 0.00889  
rotated from previous position = 0.0507 degrees  
atoms outside contour = 1405, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03103521 0.12429930 -0.99175940 96.30395985  
-0.55556537 0.82269567 0.12049553 92.31427512  
0.83089356 0.55472671 0.04352385 66.56786778  
Axis 0.21785657 -0.91443668 -0.34109246  
Axis point 40.42775437 -0.00000000 73.99767909  
Rotation angle (degrees) 94.72698175  
Shift along axis -86.14090768  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.00704  
rotated from previous position = 0.00531 degrees  
atoms outside contour = 1403, contour level = 0.1818  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03096377 0.12427425 -0.99176477 96.30211072  
-0.55561143 0.82267376 0.12043278 92.31610524  
0.83086543 0.55476482 0.04357511 66.57450729  
Axis 0.21790626 -0.91442144 -0.34110158  
Axis point 40.42531631 0.00000000 74.00490304  
Rotation angle (degrees) 94.72408447  
Shift along axis -86.13966327  
  

> volume #1 level 0.1301

> ui tool show AlphaFold

> alphafold predict #8/B

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  

> alphafold predict
> MSEYATILPENKINVIFRSNNKYHVPEFITVFKPYEGRDINLQVLVVNGDNEIYDLTKLLFYEIYVKDDTKYPWPYTKTRGGISRVFGIRYNFDPSTISRININSENDFISSISNQLDMNRFNVAVIIANRKLTKEFHDKTKAALIGSRIRTQFVTFTTLKRLKNRKYKATIPLPLAVQLIAKAGGTPWIVDSSIYNDLSKNVSSNGMLMGIAFARTRKDKITYSVGYFTTLNNYYQRFDVQPINESAPITDSTEGLYVPKEAMVKTLESGIGWYKNIIGITPPLLIIFKTSPMHKDEKEAIEAVLGKDIKWVFIHAQYNTPVRIFGNKEDDYKVNRGTVIIKKRKRWNPNNGDYLHSEIVITATGKYRKPSTKNPSETEERYISGTPRPITLNVYSSFDVNPIGVAELTLSQIKADWEHPDIRKRKITVLKYANRMAKIIQYINNLSSVPSVDVRDVL

Running AlphaFold prediction  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 52  
shifted from previous position = 4.63  
rotated from previous position = 0.0825 degrees  
atoms outside contour = 1023, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.02999734 0.12485251 -0.99172185 96.32022999  
-0.55635644 0.82218410 0.12033714 92.30100403  
0.83040222 0.55536056 0.04479916 66.53693205  
Axis 0.21823782 -0.91410339 -0.34174150  
Axis point 40.46881965 0.00000000 74.03854111  
Rotation angle (degrees) 94.67519542  
Shift along axis -86.09037444  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.0497  
rotated from previous position = 0.0411 degrees  
atoms outside contour = 1018, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03065665 0.12486176 -0.99170052 96.29089340  
-0.55611173 0.82229303 0.12072342 92.32755120  
0.83054205 0.55519719 0.04422834 66.56456703  
Axis 0.21797214 -0.91420503 -0.34163914  
Axis point 40.44870314 0.00000000 73.99649405  
Rotation angle (degrees) 94.70742345  
Shift along axis -86.15864207  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.0158  
rotated from previous position = 0.0635 degrees  
atoms outside contour = 1019, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03120173 0.12421953 -0.99176417 96.30190722  
-0.55552386 0.82271957 0.12052376 92.31567692  
0.83091509 0.55470913 0.04333664 66.57240819  
Axis 0.21783657 -0.91446240 -0.34103629  
Axis point 40.42514889 0.00000000 73.99028073  
Rotation angle (degrees) 94.73646323  
Shift along axis -86.14474540  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 56  
shifted from previous position = 4.21  
rotated from previous position = 0.0674 degrees  
atoms outside contour = 1931, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28462104 0.60554971 -0.74316930 93.46345205  
0.80434960 -0.27091387 -0.52879827 93.53980628  
-0.52154844 -0.74827494 -0.40996582 97.96979467  
Axis -0.59338134 -0.59917838 0.53747917  
Axis point -9.67301333 0.00000000 95.49541560  
Rotation angle (degrees) 169.34252404  
Shift along axis -58.84977390  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 44  
shifted from previous position = 0.006  
rotated from previous position = 0.0179 degrees  
atoms outside contour = 1930, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28441427 0.60573168 -0.74310015 93.46649937  
0.80430371 -0.27106123 -0.52879255 93.53320929  
-0.52173198 -0.74807426 -0.41009850 97.97042134  
Axis -0.59347929 -0.59912624 0.53742914  
Axis point -9.67006527 0.00000000 95.48750788  
Rotation angle (degrees) 169.35387973  
Shift along axis -58.85647249  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 48  
shifted from previous position = 0.0166  
rotated from previous position = 0.04 degrees  
atoms outside contour = 1932, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28484492 0.60525531 -0.74332333 93.45754588  
0.80435946 -0.27088059 -0.52880031 93.54981671  
-0.52141099 -0.74852514 -0.40968382 97.97089944  
Axis -0.59327360 -0.59918006 0.53759622  
Axis point -9.68563318 0.00000000 95.51648504  
Rotation angle (degrees) 169.32837268  
Shift along axis -58.83029407  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 64  
shifted from previous position = 3.89  
rotated from previous position = 0.0328 degrees  
atoms outside contour = 1932, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28490365 0.60495022 -0.74354915 93.45571001  
0.80418220 -0.27129206 -0.52885897 93.54474974  
-0.52165226 -0.74862275 -0.40919805 97.97041634  
Axis -0.59324649 -0.59900475 0.53782145  
Axis point -9.69984169 0.00000000 95.54826664  
Rotation angle (degrees) 169.32596530  
Shift along axis -58.78543018  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 48  
shifted from previous position = 0.0432  
rotated from previous position = 0.0759 degrees  
atoms outside contour = 1922, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28393956 0.60567639 -0.74332673 93.47725637  
0.80405390 -0.27194232 -0.52872006 93.50154394  
-0.52237519 -0.74779920 -0.40978123 97.97497605  
Axis -0.59369322 -0.59876731 0.53759285  
Axis point -9.68557439 0.00000000 95.51219970  
Rotation angle (degrees) 169.36770614  
Shift along axis -58.81183499  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 48  
shifted from previous position = 0.0424  
rotated from previous position = 0.0702 degrees  
atoms outside contour = 1930, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28466918 0.60547632 -0.74321065 93.46030719  
0.80438443 -0.27086696 -0.52876931 93.54678443  
-0.52146844 -0.74835131 -0.40992820 97.96825119  
Axis -0.59335587 -0.59919321 0.53749075  
Axis point -9.67999822 0.00000000 95.49977496  
Rotation angle (degrees) 169.33688696  
Shift along axis -58.85079137  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 72  
shifted from previous position = 7.58  
rotated from previous position = 0.0094 degrees  
atoms outside contour = 1020, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03129680 0.12430634 -0.99175030 96.30305046  
-0.55560351 0.82264811 0.12064427 92.31435583  
0.83085825 0.55479566 0.04331878 66.56932244  
Axis 0.21782119 -0.91443394 -0.34112242  
Axis point 40.43192855 0.00000000 73.98066354  
Rotation angle (degrees) 94.74176381  
Shift along axis -86.14682309  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.00405  
rotated from previous position = 0.0211 degrees  
atoms outside contour = 1021, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03093041 0.12427036 -0.99176630 96.30250714  
-0.55561038 0.82267763 0.12041113 92.31590775  
0.83086738 0.55475994 0.04360014 66.57323445  
Axis 0.21791411 -0.91442083 -0.34109822  
Axis point 40.42549180 0.00000000 74.00666615  
Rotation angle (degrees) 94.72229457  
Shift along axis -86.13792513  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.00377  
rotated from previous position = 0.00865 degrees  
atoms outside contour = 1018, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03090068 0.12437903 -0.99175361 96.30201984  
-0.55569100 0.82261301 0.12048056 92.31619056  
0.83081456 0.55483141 0.04369701 66.57708386  
Axis 0.21791457 -0.91438561 -0.34119231  
Axis point 40.42736468 0.00000000 74.00744858  
Rotation angle (degrees) 94.72051328  
Shift along axis -86.14257185  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 48  
shifted from previous position = 0.0497  
rotated from previous position = 0.063 degrees  
atoms outside contour = 1022, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03026295 0.12491332 -0.99170612 96.32005642  
-0.55628371 0.82220378 0.12053873 92.30171986  
0.83044131 0.55531774 0.04460493 66.53564920  
Axis 0.21811915 -0.91413163 -0.34174170  
Axis point 40.47032821 0.00000000 74.01997921  
Rotation angle (degrees) 94.68784685  
Shift along axis -86.10467886  
  

> view

> cofr frontCenter

> ui tool show "Side View"

> view orient

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 56  
shifted from previous position = 3.89  
rotated from previous position = 0.00933 degrees  
atoms outside contour = 1019, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03028762 0.12488642 -0.99170875 96.32425006  
-0.55615220 0.82229298 0.12053715 92.29707511  
0.83052849 0.55519172 0.04455056 66.52131139  
Axis 0.21805663 -0.91417631 -0.34166208  
Axis point 40.47186834 0.00000000 74.01482981  
Rotation angle (degrees) 94.68755530  
Shift along axis -86.09946863  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.0602  
rotated from previous position = 0.0983 degrees  
atoms outside contour = 1020, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03148495 0.12412770 -0.99176672 96.30144748  
-0.55534912 0.82282438 0.12061348 92.31542625  
0.83102120 0.55457420 0.04302762 66.56969721  
Axis 0.21772828 -0.91453547 -0.34090947  
Axis point 40.42181780 -0.00000000 73.97382706  
Rotation angle (degrees) 94.75047463  
Shift along axis -86.15242362  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.0469  
rotated from previous position = 0.0928 degrees  
atoms outside contour = 1023, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03045822 0.12487696 -0.99170472 96.32335142  
-0.55617924 0.82226218 0.12062243 92.28825311  
0.83050414 0.55523945 0.04440932 66.54516815  
Axis 0.21804087 -0.91417497 -0.34167572  
Axis point 40.46180126 -0.00000000 74.01692293  
Rotation angle (degrees) 94.69740388  
Shift along axis -86.10205246  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 52  
shifted from previous position = 2.67  
rotated from previous position = 0.0802 degrees  
atoms outside contour = 1923, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28375365 0.60596235 -0.74316464 93.48662197  
0.80405927 -0.27192048 -0.52872312 93.48252375  
-0.52246793 -0.74757544 -0.41007116 97.97279847  
Axis -0.59378347 -0.59878761 0.53747054  
Axis point -9.66444175 0.00000000 95.48545371  
Rotation angle (degrees) 169.38047536  
Shift along axis -58.82949460  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 40  
shifted from previous position = 0.0702  
rotated from previous position = 0.0891 degrees  
atoms outside contour = 1933, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28485856 0.60520610 -0.74335817 93.45590405  
0.80429469 -0.27099463 -0.52884040 93.55276831  
-0.52150344 -0.74852365 -0.40956886 97.97077379  
Axis -0.59326955 -0.59913377 0.53765227  
Axis point -9.68993821 0.00000000 95.52519175  
Rotation angle (degrees) 169.33034215  
Shift along axis -58.82095699  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 44  
shifted from previous position = 0.00203  
rotated from previous position = 0.0234 degrees  
atoms outside contour = 1931, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28502403 0.60494137 -0.74351021 93.45252992  
0.80418867 -0.27116617 -0.52891369 93.55198686  
-0.52157652 -0.74867551 -0.40919807 97.96997164  
Axis -0.59319456 -0.59905701 0.53782052  
Axis point -9.69692559 0.00000000 95.54738419  
Rotation angle (degrees) 169.32511613  
Shift along axis -58.78824441  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 48  
shifted from previous position = 0.0681  
rotated from previous position = 0.064 degrees  
atoms outside contour = 1923, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28450875 0.60568569 -0.74310148 93.48619046  
0.80445389 -0.27078212 -0.52870709 93.49309098  
-0.52144884 -0.74821257 -0.41020628 97.97449346  
Axis -0.59342857 -0.59923334 0.53736574  
Axis point -9.63755371 0.00000000 95.46532436  
Rotation angle (degrees) 169.34196696  
Shift along axis -58.85341701  
  

> ui tool show "Side View"

> view

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 80  
shifted from previous position = 15.6  
rotated from previous position = 0.0171 degrees  
atoms outside contour = 1930, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28442666 0.60578749 -0.74304992 93.46694182  
0.80432022 -0.27098520 -0.52880640 93.53321029  
-0.52169977 -0.74805662 -0.41017167 97.97023743  
Axis -0.59347534 -0.59915953 0.53739640  
Axis point -9.66509813 0.00000000 95.48140432  
Rotation angle (degrees) 169.35535483  
Shift along axis -58.86278610  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 48  
shifted from previous position = 0.0118  
rotated from previous position = 0.0538 degrees  
atoms outside contour = 1930, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28503772 0.60516525 -0.74332275 93.45926243  
0.80415768 -0.27103737 -0.52902682 93.54324145  
-0.52161682 -0.74854120 -0.40939235 97.96802855  
Axis -0.59319965 -0.59912191 0.53774261  
Axis point -9.67192833 0.00000000 95.52594396  
Rotation angle (degrees) 169.33736835  
Shift along axis -58.80222300  
  

> fitmap #2 inMap #1

Fit molecule SisAgo.pdb (#2) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms  
average map value = 0.1314, steps = 48  
shifted from previous position = 0.00535  
rotated from previous position = 0.0751 degrees  
atoms outside contour = 1934, contour level = 0.13014  
  
Position of SisAgo.pdb (#2) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28400058 0.60569414 -0.74328896 93.46313390  
0.80403423 -0.27189572 -0.52877394 93.53401577  
-0.52237229 -0.74780178 -0.40978022 97.97373349  
Axis -0.59366914 -0.59878875 0.53759556  
Axis point -9.70323338 0.00000000 95.52230007  
Rotation angle (degrees) 169.36978891  
Shift along axis -58.82305128  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 96  
shifted from previous position = 15.7  
rotated from previous position = 0.0765 degrees  
atoms outside contour = 1019, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03125010 0.12419508 -0.99176571 96.30208056  
-0.55549429 0.82273835 0.12053180 92.31537729  
0.83093303 0.55468675 0.04327900 66.57108185  
Axis 0.21782209 -0.91447549 -0.34101042  
Axis point 40.42496810 0.00000000 73.98732537  
Rotation angle (degrees) 94.73897069  
Shift along axis -86.14486199  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.002  
rotated from previous position = 0.0193 degrees  
atoms outside contour = 1021, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03092915 0.12423425 -0.99177086 96.30313189  
-0.55557791 0.82270380 0.12038219 92.31537346  
0.83088914 0.55472922 0.04357628 66.57054592  
Axis 0.21791319 -0.91443390 -0.34106376  
Axis point 40.42519409 -0.00000000 74.00667820  
Rotation angle (degrees) 94.72219238  
Shift along axis -86.13538519  
  

> fitmap #3 inMap #1

Fit molecule best_model.pdb (#3) to map
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms  
average map value = 0.1282, steps = 44  
shifted from previous position = 0.00425  
rotated from previous position = 0.00651 degrees  
atoms outside contour = 1020, contour level = 0.13014  
  
Position of best_model.pdb (#3) relative to
cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.03091175 0.12431226 -0.99176163 96.30229822  
-0.55564285 0.82265237 0.12043385 92.31612211  
0.83084635 0.55478801 0.04364359 66.57477090  
Axis 0.21791646 -0.91440654 -0.34113501  
Axis point 40.42617267 0.00000000 74.00742776  
Rotation angle (degrees) 94.72123576  
Shift along axis -86.13959472  
  

> cofr frontCenter


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold




OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
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: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 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 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 1 day, 20 hours, 43 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        Sceptre F27:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55


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: 1.5
    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: 1.6.4
    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: 5.1.0
    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: 5.1.0
    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: 3.0.33
    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: 0.6.2
    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: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Graphics hardware encountered an error and was reset

comment:2 by Tom Goddard, 3 years ago

Resolution: → nonchimerax
Status: assigned → closed
Summary: Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics

Apple Intel graphics driver crash.

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