id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15935	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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    ""CFBundleIdentifier"" : ""org.python.python"",
    ""size"" : 4030464,
    ""uuid"" : ""514efc82-c424-3863-84a8-e24ffd50343d"",
    ""path"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python"",
    ""name"" : ""Python"",
    ""CFBundleVersion"" : ""3.11.4""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64"",
    ""base"" : 140703125831680,
    ""size"" : 196608,
    ""uuid"" : ""b091dec9-37ac-322a-bd9d-fc5dc22b0082"",
    ""path"" : ""\/usr\/libexec\/rosetta\/runtime"",
    ""name"" : ""runtime""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64"",
    ""base"" : 4501344256,
    ""size"" : 344064,
    ""uuid"" : ""8a85f070-3849-3b55-adde-143cc5902f92"",
    ""path"" : ""\/Library\/Apple\/*\/libRosettaRuntime"",
    ""name"" : ""libRosettaRuntime""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 4366987264,
    ""CFBundleShortVersionString"" : ""1.8.0"",
    ""CFBundleIdentifier"" : ""edu.ucsf.cgl.ChimeraX"",
    ""size"" : 16384,
    ""uuid"" : ""194a3167-3db5-3029-8d22-1d742b826bb9"",
    ""path"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"",
    ""name"" : ""ChimeraX"",
    ""CFBundleVersion"" : ""1.8.0.0""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703608205312,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.AppKit"",
    ""size"" : 21164019,
    ""uuid"" : ""33ecd3dc-c895-35e2-a1fd-c1761b155964"",
    ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"",
    ""name"" : ""AppKit"",
    ""CFBundleVersion"" : ""2487.60.105""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703641534464,
    ""CFBundleShortVersionString"" : ""1.600.0"",
    ""CFBundleIdentifier"" : ""com.apple.SkyLight"",
    ""size"" : 4595703,
    ""uuid"" : ""c85f48c7-7d13-316b-a28b-cfbd2693b663"",
    ""path"" : ""\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight"",
    ""name"" : ""SkyLight""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703549407232,
    ""size"" : 290802,
    ""uuid"" : ""511b909b-7a60-3295-9981-a508477c7893"",
    ""path"" : ""\/usr\/lib\/system\/libdispatch.dylib"",
    ""name"" : ""libdispatch.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703551524864,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"",
    ""size"" : 4825085,
    ""uuid"" : ""a32f4005-d666-32c2-8e52-f67fc64616e0"",
    ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"",
    ""name"" : ""CoreFoundation"",
    ""CFBundleVersion"" : ""2503.1""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703735283712,
    ""CFBundleShortVersionString"" : ""2.1.1"",
    ""CFBundleIdentifier"" : ""com.apple.HIToolbox"",
    ""size"" : 2732020,
    ""uuid"" : ""de4aeb8b-676c-3a36-9364-1cdee78a3b41"",
    ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"",
    ""name"" : ""HIToolbox""
  },
  {
    ""size"" : 0,
    ""source"" : ""A"",
    ""base"" : 0,
    ""uuid"" : ""00000000-0000-0000-0000-000000000000""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703550861312,
    ""size"" : 241656,
    ""uuid"" : ""13597eeb-2ea0-3d48-8be1-dfc4872a784b"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"",
    ""name"" : ""libsystem_kernel.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703551102976,
    ""size"" : 49144,
    ""uuid"" : ""25b2f3eb-07b4-3cb9-9457-2c26210c27c8"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"",
    ""name"" : ""libsystem_pthread.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703550267392,
    ""size"" : 503796,
    ""uuid"" : ""e443af07-488b-3b1b-83ae-31bd883e6ef1"",
    ""path"" : ""\/usr\/lib\/libc++.1.dylib"",
    ""name"" : ""libc++.1.dylib""
  }
],
  ""sharedCache"" : {
  ""base"" : 140703546687488,
  ""size"" : 25769803776,
  ""uuid"" : ""6f51a82c-c96c-3bc8-82ca-9c109185bd3c""
},
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""logWritingSignature"" : ""0103e84532159ea8501c1b484aed04127e7bc428"",
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""645197bf528fbf3c3af54105"",
      ""factorPackIds"" : {
        ""SIRI_VALUE_INFERENCE_PERVASIVE_ENTITY_RESOLUTION"" : ""663e65b4a1526e1ca0e288a1""
      },
      ""deploymentId"" : 240000002
    },
    {
      ""rolloutId"" : ""62745b8e85854550ad70b6e4"",
      ""factorPackIds"" : {
        ""SIRI_TTS_DEVICE_TRAINING"" : ""6539d7f333b9b7499c6f1b63""
      },
      ""deploymentId"" : 240000073
    }
  ],
  ""experiments"" : [
    {
      ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"",
      ""experimentId"" : ""6639bc6ba73d460582162323"",
      ""deploymentId"" : 400000006
    },
    {
      ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"",
      ""experimentId"" : ""6643969b3099cf28e049862f"",
      ""deploymentId"" : 400000007
    }
  ]
},
  ""reportNotes"" : [
  ""PC register does not match crashing frame (0x0 vs 0x1492CE944)""
]
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jana/Downloads/cryosparc_P4_J3466_map.mrc format mrc

Opened cryosparc_P4_J3466_map.mrc as #1, grid size 288,288,288, pixel 1.66,
shown at level 0.024, step 2, values float32  

> color cornflower blue

> lighting soft

> close

> open
> ""/Users/jana/Downloads/cryosparc_P4_J3550_volume_multi_ds/cryosparc_P4_J3547_map
> (1).mrc""

Opened cryosparc_P4_J3547_map (1).mrc as #1, grid size 576,576,576, pixel
0.83, shown at level 0.00826, step 4, values float32  

> open
> /Users/jana/Downloads/cryosparc_P4_J3550_volume_multi_ds/J3550_map_aligned_0.mrc

Opened J3550_map_aligned_0.mrc as #2, grid size 576,576,576, pixel 0.83, shown
at level 0.00926, step 4, values float32  

> open
> /Users/jana/Downloads/cryosparc_P4_J3550_volume_multi_ds/J3550_map_aligned_1.mrc

Opened J3550_map_aligned_1.mrc as #3, grid size 576,576,576, pixel 0.83, shown
at level 0.00824, step 4, values float32  

> open
> /Users/jana/Downloads/cryosparc_P4_J3550_volume_multi_ds/J3550_map_aligned_2.mrc

Opened J3550_map_aligned_2.mrc as #4, grid size 576,576,576, pixel 0.83, shown
at level 0.00894, step 4, values float32  

> open
> /Users/jana/Downloads/cryosparc_P4_J3550_volume_multi_ds/J3550_map_aligned_3.mrc

Opened J3550_map_aligned_3.mrc as #5, grid size 576,576,576, pixel 0.83, shown
at level 0.00917, step 4, values float32  

> open
> /Users/jana/Downloads/cryosparc_P4_J3550_volume_multi_ds/J3550_map_aligned_4.mrc

Opened J3550_map_aligned_4.mrc as #6, grid size 576,576,576, pixel 0.83, shown
at level 0.00827, step 4, values float32  

> open
> /Users/jana/Downloads/cryosparc_P4_J3550_volume_multi_ds/J3550_map_aligned_5.mrc

Opened J3550_map_aligned_5.mrc as #7, grid size 576,576,576, pixel 0.83, shown
at level 0.00837, step 4, values float32  

> set bgColor white

> set bgColor #ffffff00

> surface dust #1 size 8.3

> surface dust #2 size 8.3

> surface dust #3 size 8.3

> surface dust #4 size 8.3

> surface dust #5 size 8.3

> surface dust #6 size 8.3

> surface dust #7 size 8.3

> color cornflower blue

> tile

7 models tiled  

> hide #!7 models

> show #!7 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> hide #!1 models

> hide #!6 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!4 models

> volume resample #1 onGrid #1

Opened cryosparc_P4_J3547_map (1).mrc resampled as #8, grid size 576,576,576,
pixel 0.83, shown at step 1, values float32  

> volume resample #2 onGrid #1

Opened J3550_map_aligned_0.mrc resampled as #9, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #3 onGrid #1

Opened J3550_map_aligned_1.mrc resampled as #10, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #4 onGrid #1

Opened J3550_map_aligned_2.mrc resampled as #11, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> close #11

> close #10

> close #9

> close #8

> show #!6 models

> show #!7 models

> show #!4 models

> show #!3 models

> show #!2 models

> show #!1 models

> tile off

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> volume resample #1 onGrid #1

Opened cryosparc_P4_J3547_map (1).mrc resampled as #8, grid size 576,576,576,
pixel 0.83, shown at step 1, values float32  

> volume resample #2 onGrid #1

Opened J3550_map_aligned_0.mrc resampled as #9, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #3 onGrid #1

Opened J3550_map_aligned_1.mrc resampled as #10, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #4 onGrid #1

Opened J3550_map_aligned_2.mrc resampled as #11, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #5 onGrid #1

Opened J3550_map_aligned_3.mrc resampled as #12, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #6 onGrid #1

Opened J3550_map_aligned_4.mrc resampled as #13, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #7 onGrid #1

Opened J3550_map_aligned_5.mrc resampled as #14, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> color #8-14 cornflower blue

> surface dust #8 size 8.3

> surface dust #9 size 8.3

> surface dust #10 size 8.3

> surface dust #11 size 8.3

> surface dust #12 size 8.3

> surface dust #13 size 8.3

> surface dust #14 size 8.3

> lighting simple

> lighting soft

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #14 step 4

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #13 step 4

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #12 step 4

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #11 step 4

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #10 step 4

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #9 step 4

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #8 step 4

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!8 models

> show #!9 models

> hide #!8 models

> hide #!9 models

> show #!8 models

> show #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> tile

7 models tiled  

> hide #!8 models

> show #!8 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> hide #!10 models

> hide #!11 models

> show #!11 models

> show #!1 models

> hide #!1 models

> hide #!8 models

> show #!8 models

> hide #!13 models

> show #!13 models

> hide #!8 models

> show #!8 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> hide #!8 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> hide #!11 models

> hide #!12 models

> show #!11 models

> show #!12 models

> hide #!12 models

> hide #!11 models

> show #!9 models

> show #!10 models

> show #!8 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> tile off

> hide #!8 models

> hide #!9 models

> hide #!11 models

> hide #!10 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> volume morph #12 #11 #14 #8 #13 #10 #9

Map positions are not the same, J3550_map_aligned_2.mrc resampled #11 and
J3550_map_aligned_3.mrc resampled #12. Use the ""volume resample"" command to
make a copy of one map with the same grid as the other map.  

> close #14

> close #13

> close #12

> close #11

> close #10

> close #9

> close #8

> volume resample #1 onGrid #7

Opened cryosparc_P4_J3547_map (1).mrc resampled as #8, grid size 576,576,576,
pixel 0.83, shown at step 1, values float32  

> volume resample #2 onGrid #7

Opened J3550_map_aligned_0.mrc resampled as #9, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #3 onGrid #7

Opened J3550_map_aligned_1.mrc resampled as #10, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #4 onGrid #7

Opened J3550_map_aligned_2.mrc resampled as #11, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #5 onGrid #7

Opened J3550_map_aligned_3.mrc resampled as #12, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #6 onGrid #7

Opened J3550_map_aligned_4.mrc resampled as #13, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> volume resample #7 onGrid #7

Opened J3550_map_aligned_5.mrc resampled as #14, grid size 576,576,576, pixel
0.83, shown at step 1, values float32  

> surface dust #8 size 8.3

> surface dust #9 size 8.3

> surface dust #10 size 8.3

> surface dust #11 size 8.3

> surface dust #12 size 8.3

> surface dust #13 size 8.3

> surface dust #14 size 8.3

> color #8-14 cornflower blue

> volume morph #12 #11 #14 #8 #13 #10 #9

Opened morph as #15, grid size 576,576,576, pixel 0.83, shown at step 1,
values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #15 step 4

> surface dust #15 size 8.3

> volume #15 level 0.02905

> lighting soft

> volume #15 level 0.0345

> volume #15 level 0.03482

> volume #15 step 2

> volume #15 level 0.04114

> movie record

> movie encode /Users/jana/Desktop/movie13.mp4 framerate 25.0

Movie saved to /Users/jana/Desktop/movie13.mp4  
  

> movie record

> movie encode /Users/jana/Desktop/movie13.mp4 framerate 25.0

Error processing trigger ""new frame"":  
Movie encoding failed because no images were recorded.  

> movie record

> movie encode /Users/jana/Desktop/movie13.mp4 framerate 25.0

Movie saved to /Users/jana/Desktop/movie13.mp4  
  

> movie record

> movie encode /Users/jana/Desktop/movie13.mp4 framerate 25.0

Movie saved to /Users/jana/Desktop/movie13.mp4  
  

> movie record

> movie encode /Users/jana/Desktop/movie13.mp4 framerate 25.0

Movie saved to /Users/jana/Desktop/movie13.mp4  
  

> movie record

> movie encode /Users/jana/Desktop/movie14.mp4 framerate 25.0

Movie saved to /Users/jana/Desktop/movie14.mp4  
  

> movie record

> movie encode /Users/jana/Desktop/movie15.mp4 framerate 25.0

Movie saved to /Users/jana/Desktop/movie15.mp4  
  

> movie record

> movie encode /Users/jana/Desktop/movie16.mp4 framerate 25.0

Movie saved to /Users/jana/Desktop/movie16.mp4  
  

> close

> open /Users/jana/Downloads/cryosparc_P4_J2818_004_volume_map.mrc

Opened cryosparc_P4_J2818_004_volume_map.mrc as #1, grid size 576,576,576,
pixel 0.83, shown at level 0.0171, step 4, values float32  

> color #1 #785ebfff models

> surface dust #1 size 8.3

> volume #1 level 0.03003

> volume #1 level 0.03238

> volume #1 level 0.02

> volume #1 level 0.01

> volume #1 level 0.025

> volume #1 level 0.03

> volume #1 level 0.05461

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #1 step 2

> volume #1 step 4

> open /Users/jana/Downloads/cryosparc_P4_J2155_008_volume_map_sharp.mrc

Opened cryosparc_P4_J2155_008_volume_map_sharp.mrc as #2, grid size
576,576,576, pixel 0.83, shown at level 0.0114, step 4, values float32  

> volume #2 color #5152ff

> volume #2 color #817bff

> volume #2 color #ff96ec

> volume #2 color #63ff43

> volume #2 color #5762ff

> volume #2 color #7d91ff

> surface dust #1 size 8.3

> surface dust #2 size 8.3

> volume #2 level 0.02

> select add #2

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.99207,-0.12361,0.022909,27.343,-0.12535,-0.95887,0.25467,456.22,-0.0095132,-0.25552,-0.96676,482.08

> volume #2 level 0.02641

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.99207,-0.12361,0.022909,24.899,-0.12535,-0.95887,0.25467,444.13,-0.0095132,-0.25552,-0.96676,519.22

> volume #2 level 0.04563

> fitmap #2 inMap #1

Fit map cryosparc_P4_J2155_008_volume_map_sharp.mrc in map
cryosparc_P4_J2818_004_volume_map.mrc using 8030 points  
correlation = 0.8573, correlation about mean = 0.5672, overlap = 62.76  
steps = 188, shift = 8.68, angle = 13.5 degrees  
  
Position of cryosparc_P4_J2155_008_volume_map_sharp.mrc (#2) relative to
cryosparc_P4_J2818_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99917232 -0.00946997 -0.03955993 11.18307829  
-0.00704964 -0.99812026 0.06087890 465.89082054  
-0.04006209 -0.06054963 -0.99736090 494.63692145  
Axis -0.99979287 0.00413458 0.01992801  
Axis point 0.00000000 240.48627912 240.34893058  
Rotation angle (degrees) 176.51846610  
Shift along axis 0.60262989  
  

> select subtract #2

Nothing selected  

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #2 level 0.01199

> show #!1 models

> volume #2 level 0.04162

> tile

2 models tiled  

> tile off

> select add #2

2 models selected  

> view matrix models
> #2,0.99919,0.037675,-0.013796,-4.5787,-0.037606,0.99928,0.0052042,7.3627,0.013982,-0.0046812,0.99989,8.8619

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.74948,0.66021,-0.049039,285.19,0.65925,0.75106,0.035886,-111.79,0.060524,-0.0054336,-0.99815,443.77

> view matrix models
> #2,-0.72126,0.69223,-0.024455,264.84,0.69092,0.7215,0.045489,-114.56,0.049133,0.015913,-0.99867,441.49

> ui mousemode right ""move picked models""

> view matrix models
> #2,-0.72126,0.69223,-0.024455,260.58,0.69092,0.7215,0.045489,-102.67,0.049133,0.015913,-0.99867,452.91

> fitmap #2 inMap #1

Fit map cryosparc_P4_J2155_008_volume_map_sharp.mrc in map
cryosparc_P4_J2818_004_volume_map.mrc using 9050 points  
correlation = 0.8482, correlation about mean = 0.57, overlap = 64.74  
steps = 212, shift = 10.6, angle = 18.8 degrees  
  
Position of cryosparc_P4_J2155_008_volume_map_sharp.mrc (#2) relative to
cryosparc_P4_J2818_004_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.49142794 0.87004143 -0.03907037 157.21475217  
0.86769872 0.49297217 0.06385436 -100.21752844  
0.07481654 -0.00252149 -0.99719413 453.25903961  
Axis -0.50346218 -0.86383452 -0.01776950  
Axis point 99.15561706 0.00000000 230.65671920  
Rotation angle (degrees) 176.22035568  
Shift along axis -0.63450745  
  

> select subtract #2

Nothing selected  

> lighting soft

> volume #2 level 0.05203

> volume #2 level 0.05123

> tile

2 models tiled  

> undo

> lighting soft

> fitmap #1 inMap #2

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map_sharp.mrc using 7699 points  
correlation = 0.8733, correlation about mean = 0.5266, overlap = 62.47  
steps = 60, shift = 0.154, angle = 0.189 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.48950701 0.86888785 0.07359882 129.91063775  
0.87106902 0.49113770 -0.00474455 -85.37922390  
-0.04026964 0.06178717 -0.99727664 465.27258262  
Axis 0.50441544 0.86330273 0.01653672  
Axis point 98.79384786 0.00000000 230.96560700  
Rotation angle (degrees) 176.21863755  
Shift along axis -0.48510267  
  

> fitmap #1 inMap #2

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map_sharp.mrc using 7699 points  
correlation = 0.8734, correlation about mean = 0.5267, overlap = 62.47  
steps = 80, shift = 0.00628, angle = 0.00419 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.48950874 0.86888747 0.07359182 129.91133843  
0.87106527 0.49114365 -0.00481701 -85.36244954  
-0.04032959 0.06174532 -0.99727681 465.30304426  
Axis 0.50441383 0.86330430 0.01650357  
Axis point 98.79386840 0.00000000 230.97786856  
Rotation angle (degrees) 176.21688345  
Shift along axis -0.48553266  
  

> fitmap #1 inMap #2

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map_sharp.mrc using 7699 points  
correlation = 0.8733, correlation about mean = 0.5265, overlap = 62.47  
steps = 120, shift = 0.0102, angle = 0.0101 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.48950835 0.86889804 0.07346948 129.94456874  
0.87106314 0.49114616 -0.00494427 -85.32435934  
-0.04038032 0.06157630 -0.99728521 465.35640396  
Axis 0.50441504 0.86330523 0.01641764  
Axis point 98.79477826 0.00000000 231.00097793  
Rotation angle (degrees) 176.21926916  
Shift along axis -0.47491735  
  

> fitmap #1 inMap #2

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map_sharp.mrc using 7699 points  
correlation = 0.8734, correlation about mean = 0.5267, overlap = 62.47  
steps = 64, shift = 0.0152, angle = 0.00914 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.48951426 0.86889050 0.07351932 129.93557816  
0.87106479 0.49114474 -0.00479279 -85.36923918  
-0.04027304 0.06169395 -0.99728228 465.31452982  
Axis 0.50441292 0.86330498 0.01649564  
Axis point 98.79800691 0.00000000 230.98567699  
Rotation angle (degrees) 176.22117837  
Shift along axis -0.48284174  
  

> volume #1 level 0.06751

> volume #2 level 0.05123

> volume #1 step 2

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #2 step 2

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> volume #1 level 0.06618

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> ui tool show ""Side View""

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> ui tool show ""Side View""

> open /Users/jana/Downloads/cryosparc_P4_J2154_006_volume_map_sharp.mrc

Opened cryosparc_P4_J2154_006_volume_map_sharp.mrc as #3, grid size
576,576,576, pixel 0.83, shown at level 0.0108, step 4, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #3 step 2

> surface dust #2 size 8.3

> surface dust #3 size 8.3

> volume #3 level 0.04239

> color #3 #ff3431ff models

> color #3 #ff6d62ff models

> color #3 #ff9281ff models

> select add #3

3 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,-0.99856,0.048375,-0.02332,451.76,0.050148,0.99532,-0.082638,9.3084,0.019213,-0.083688,-0.99631,490.91

> view matrix models
> #3,0.72285,0.69085,-0.014501,-103.91,0.68776,-0.71728,0.11181,240.54,0.06684,-0.090793,-0.99362,481.11

> select subtract #3

Nothing selected  

> hide #!3 models

> hide #!2 models

> show #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> fitmap #2 inMap #3

Fit map cryosparc_P4_J2155_008_volume_map_sharp.mrc in map
cryosparc_P4_J2154_006_volume_map_sharp.mrc using 55028 points  
correlation = 0.5991, correlation about mean = 0.1146, overlap = 143  
steps = 276, shift = 11, angle = 8.61 degrees  
  
Position of cryosparc_P4_J2155_008_volume_map_sharp.mrc (#2) relative to
cryosparc_P4_J2154_006_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.13975348 0.99007986 -0.01452094 -25.06555740  
-0.98811789 0.14039394 0.06255079 443.78814909  
0.06396893 0.00560671 0.99793615 -10.33369132  
Axis -0.02875132 -0.03962988 -0.99880070  
Axis point 242.99881270 236.64013045 0.00000000  
Rotation angle (degrees) 82.00759754  
Shift along axis -6.54530453  
  

> ui mousemode right ""translate selected models""

> select add #3

2 models selected  

> view matrix models
> #3,0.72285,0.69085,-0.014501,-96.1,0.68776,-0.71728,0.11181,229.01,0.06684,-0.090793,-0.99362,479.15

> view matrix models
> #3,0.72285,0.69085,-0.014501,-99.025,0.68776,-0.71728,0.11181,231.51,0.06684,-0.090793,-0.99362,480.25

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,-0.99877,-0.036171,-0.033812,480.1,-0.035011,0.9988,-0.034289,7.4503,0.035011,-0.033063,-0.99884,474.51

> ui mousemode right ""translate selected models""

> view matrix models
> #3,-0.99877,-0.036171,-0.033812,501.46,-0.035011,0.9988,-0.034289,32.322,0.035011,-0.033063,-0.99884,475.18

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,-0.98462,-0.057501,0.16495,456.23,-0.055471,0.99832,0.016891,24.964,-0.16564,0.0074813,-0.98616,508.14

> fitmap #3 inMap #2

Fit map cryosparc_P4_J2154_006_volume_map_sharp.mrc in map
cryosparc_P4_J2155_008_volume_map_sharp.mrc using 76199 points  
correlation = 0.662, correlation about mean = 0.1636, overlap = 220.5  
steps = 320, shift = 7.04, angle = 24.9 degrees  
  
Position of cryosparc_P4_J2154_006_volume_map_sharp.mrc (#3) relative to
cryosparc_P4_J2155_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.14654941 0.98584263 -0.08147118 -13.25671755  
-0.98917852 0.14546449 -0.01912868 444.87738943  
-0.00700670 0.08339284 0.99649211 -24.53992326  
Axis 0.05180257 -0.03762577 -0.99794829  
Axis point 250.63393705 230.79376193 0.00000000  
Rotation angle (degrees) 81.70597526  
Shift along axis 7.06398662  
  

> select add #3

3 models selected  

> select subtract #3

Nothing selected  

> ui tool show ""Side View""

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 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 #!2 models

> show #!1 models

> hide #!2 models

> volume #1 level 0.04026

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> open /Users/jana/Downloads/cryosparc_P4_J3596_map.mrc

Opened cryosparc_P4_J3596_map.mrc as #4, grid size 576,576,576, pixel 0.83,
shown at level 0.00812, step 4, values float32  

> open /Users/jana/Downloads/cryosparc_P4_J2155_008_volume_map.mrc

Opened cryosparc_P4_J2155_008_volume_map.mrc as #5, grid size 576,576,576,
pixel 0.83, shown at level 0.00748, step 4, values float32  

> close #3

> close #2

> hide #!5 models

> show #!5 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #4 step 2

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #5 step 2

> surface dust #4 size 8.3

> surface dust #5 size 8.3

> select add #5

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,-0.72868,0.67499,0.11581,234.72,0.63477,0.72914,-0.25578,-35.676,-0.25709,-0.11287,-0.95977,503.21

> ui mousemode right ""translate selected models""

> view matrix models
> #5,-0.72868,0.67499,0.11581,235.41,0.63477,0.72914,-0.25578,-38.202,-0.25709,-0.11287,-0.95977,544.69

> view matrix models
> #5,-0.72868,0.67499,0.11581,234.91,0.63477,0.72914,-0.25578,-38.493,-0.25709,-0.11287,-0.95977,549.22

> fitmap #5 inMap #4

Fit map cryosparc_P4_J2155_008_volume_map.mrc in map
cryosparc_P4_J3596_map.mrc using 238785 points  
correlation = 0.951, correlation about mean = 0.8604, overlap = 362.9  
steps = 236, shift = 13.9, angle = 23.3 degrees  
  
Position of cryosparc_P4_J2155_008_volume_map.mrc (#5) relative to
cryosparc_P4_J3596_map.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.46808143 0.88367442 0.00439293 138.79973646  
0.88078966 0.46694395 -0.07856796 -66.00022371  
-0.07147975 -0.03290696 -0.99689908 495.26036448  
Axis 0.51536278 0.85635337 -0.03255946  
Axis point 95.66742830 0.00000000 244.57212538  
Rotation angle (degrees) 177.46097372  
Shift along axis -1.11270731  
  

> select subtract #5

Nothing selected  

> volume #4 level 0.01827

> volume #5 level 0.01515

> volume #4 level 0.01972

> volume #5 level 0.01917

> lighting soft

> color #5 #a08affff models

> color #5 #acb3ffff models

> color #5 #928effff models

> color #4 #54ff52ff models

> color #4 #beff89ff models

> color #4 #ffa194ff models

> color #5 #ffa69cff models

> color #5 #7b91ffff models

> color #5 #7df5ffff models

> color #5 #7fff91ff models

> color #5 #787bffff models

> volume #5 level 0.01954

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> volume #4 level 0.02806

> volume #5 level 0.03343

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!1 models

> hide #!1 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> color #4 #ff9184ff models

> color #4 #ff7e67ff models

> color #4 #ffbd7eff models

> color #4 #ffccabff models

> color #4 #ff9379ff models

> color #4 #ff4c48ff models

> color #4 #ff6478ff models

> color #4 #ffa885ff models

> color #4 #ffa46fff models

> color #4 #ff855fff models

> color #4 #ff7b5fff models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> hide #!5 models

> show #!1 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!1 models

> show #!1 models

> color #1 #6dcb7cff models

> color #1 #52895eff models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #5 step 4

> volume #1 step 4

> show #!1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> color #5 #ff7e75ff models

> color #5 #85423dff models

> color #5 #855e4eff models

> color #5 #85413bff models

> color #5 #853c49ff models

> hide #!1 models

> show #!1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4922, overlap = 53.71  
steps = 172, shift = 2.42, angle = 8.13 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49085214 0.86816992 0.07311069 130.55837617  
0.87040375 0.49233189 -0.00257414 -86.10859607  
-0.03822952 0.06237230 -0.99732051 464.56907393  
Axis 0.50378370 0.86365603 0.01732763  
Axis point 99.07085090 0.00000000 230.70463048  
Rotation angle (degrees) 176.30422872  
Shift along axis -0.54514576  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4923, overlap = 53.71  
steps = 40, shift = 0.00715, angle = 0.0055 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49085372 0.86816504 0.07315796 130.54449091  
0.87040502 0.49233007 -0.00249060 -86.13405474  
-0.03818012 0.06245454 -0.99731725 464.53601410  
Axis 0.50378294 0.86365550 0.01737568  
Axis point 99.07053991 0.00000000 230.69098728  
Rotation angle (degrees) 176.30429745  
Shift along axis -0.55243484  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4922, overlap = 53.71  
steps = 40, shift = 0.0104, angle = 0.00696 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49085244 0.86817362 0.07306470 130.57239932  
0.87040480 0.49233006 -0.00256822 -86.10923451  
-0.03820161 0.06233524 -0.99732389 464.56987678  
Axis 0.50378458 0.86365570 0.01731859  
Axis point 99.07235028 0.00000000 230.70597314  
Rotation angle (degrees) 176.30668399  
Shift along axis -0.54267593  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4922, overlap = 53.71  
steps = 48, shift = 0.00907, angle = 0.00536 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49085454 0.86817286 0.07305958 130.56767852  
0.87040729 0.49232614 -0.00247496 -86.13488095  
-0.03811784 0.06237675 -0.99732451 464.53519403  
Axis 0.50378476 0.86365481 0.01735763  
Axis point 99.06993673 0.00000000 230.69280989  
Rotation angle (degrees) 176.30963471  
Shift along axis -0.54956901  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4923, overlap = 53.71  
steps = 48, shift = 0.0153, angle = 0.0159 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49085660 0.86815250 0.07328738 130.51107131  
0.87040716 0.49232713 -0.00231866 -86.18356918  
-0.03809432 0.06265174 -0.99730817 464.46659943  
Axis 0.50378091 0.86365453 0.01748267  
Axis point 99.07033192 0.00000000 230.66167099  
Rotation angle (degrees) 176.30284335  
Shift along axis -0.56372555  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4923, overlap = 53.71  
steps = 44, shift = 0.00782, angle = 0.00595 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49085431 0.86815600 0.07326124 130.51710489  
0.87040518 0.49233014 -0.00241907 -86.15386258  
-0.03816885 0.06257955 -0.99730985 464.49733026  
Axis 0.50378138 0.86365527 0.01743266  
Axis point 99.06902145 0.00000000 230.67312443  
Rotation angle (degrees) 176.30123822  
Shift along axis -0.55772672  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4922, overlap = 53.71  
steps = 44, shift = 0.0142, angle = 0.0124 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49084954 0.86816776 0.07315369 130.54578760  
0.87040304 0.49233296 -0.00260649 -86.09748589  
-0.03827885 0.06239380 -0.99731727 464.57249850  
Axis 0.50378371 0.86365608 0.01732451  
Axis point 99.06858759 0.00000000 230.70429863  
Rotation angle (degrees) 176.30116020  
Shift along axis -0.54328383  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4923, overlap = 53.71  
steps = 40, shift = 0.00985, angle = 0.00513 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49085156 0.86816874 0.07312851 130.54911960  
0.87040573 0.49232866 -0.00252077 -86.12436209  
-0.03819172 0.06241415 -0.99731934 464.55370406  
Axis 0.50378427 0.86365514 0.01735523  
Axis point 99.06904595 0.00000000 230.69903599  
Rotation angle (degrees) 176.30488951  
Shift along axis -0.55071976  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4923, overlap = 53.71  
steps = 44, shift = 0.00597, angle = 0.0064 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49085343 0.86816195 0.07319657 130.53600242  
0.87040657 0.49232761 -0.00243239 -86.15075425  
-0.03814840 0.06251683 -0.99731457 464.51991593  
Axis 0.50378299 0.86365477 0.01741061  
Axis point 99.07144353 0.00000000 230.68482684  
Rotation angle (degrees) 176.30406512  
Shift along axis -0.55511656  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4922, overlap = 53.71  
steps = 48, shift = 0.0179, angle = 0.0115 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49085480 0.86817692 0.07300948 130.58597041  
0.87040705 0.49232640 -0.00250560 -86.12822824  
-0.03811980 0.06231808 -0.99732810 464.54908037  
Axis 0.50378530 0.86365502 0.01733173  
Axis point 99.07365743 0.00000000 230.69914403  
Rotation angle (degrees) 176.31123564  
Shift along axis -0.54634439  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4922, overlap = 53.71  
steps = 64, shift = 0.0128, angle = 0.00737 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49084997 0.86817282 0.07309071 130.56330272  
0.87040423 0.49233088 -0.00260491 -86.09931796  
-0.03824632 0.06233984 -0.99732189 464.58371088  
Axis 0.50378482 0.86365574 0.01730931  
Axis point 99.07070187 0.00000000 230.71094225  
Rotation angle (degrees) 176.30433326  
Shift along axis -0.54273544  
  

> fitmap #1 inMap #5

Fit map cryosparc_P4_J2818_004_volume_map.mrc in map
cryosparc_P4_J2155_008_volume_map.mrc using 10411 points  
correlation = 0.8817, correlation about mean = 0.4923, overlap = 53.71  
steps = 40, shift = 0.0104, angle = 0.00768 degrees  
  
Position of cryosparc_P4_J2818_004_volume_map.mrc (#1) relative to
cryosparc_P4_J2155_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.49085441 0.86816930 0.07310272 130.55850996  
0.87040656 0.49232744 -0.00247154 -86.13735907  
-0.03813620 0.06241592 -0.99732135 464.53195203  
Axis 0.50378398 0.86365502 0.01736999  
Axis point 99.07076855 0.00000000 230.69063826  
Rotation angle (degrees) 176.30759139  
Shift along axis -0.55076335  
  

> volume #4 step 4


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK193SM/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 8 days, 20 hours, 11 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        SyncMaster:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.3.5
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX