![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 days ago
Closed 6 days ago
#19432 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.7.2-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
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"modelCode" : "Mac14,2",
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"captureTime" : "2025-11-24 18:20:12.2107 +0100",
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"incident" : "15AD322F-7A07-4EAE-82AD-7E4D3F7CFB9D",
"pid" : 61788,
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"cpuType" : "ARM-64",
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"bug_type" : "309",
"procLaunch" : "2025-11-24 17:36:08.0741 +0100",
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"procExitAbsTime" : 13251975485214,
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"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"vmSummary" : "ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=3.0G written=96.9M(3%) resident=1927K(0%) swapped_out=95.0M(3%) unallocated=2.9G(97%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1264K 59 \nColorSync 704K 33 \nCoreAnimation 3264K 198 \nCoreGraphics 48K 3 \nCoreServices 624K 2 \nCoreUI image data 5648K 62 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.4G 132 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 720K 45 \nStack 158.6M 45 \nStack (graphics) 544K 1 \nStack Guard 56.0M 1 \nVM_ALLOCATE 347.1M 260 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__AUTH 6043K 723 \n__AUTH_CONST 80.4M 976 \n__CTF 824 1 \n__DATA 37.0M 1133 \n__DATA_CONST 37.7M 1149 \n__DATA_DIRTY 2788K 347 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 648.8M 168 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.4G 1153 \n__TEXT (graphics) 4416K 17 \n__TPRO_CONST 128K 2 \ndyld private memory 2848K 24 \nmapped file 600.8M 97 \npage table in kernel 1927K 1 \nshared memory 3152K 22 \n=========== ======= ======= \nTOTAL 5.9G 6692 \nTOTAL, minus reserved VM space 5.8G 6692 \n",
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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},
"logWritingSignature" : "1d87db80aad2752b37fb397f900c17e49a66c93b",
"trialInfo" : {
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{
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"factorPackIds" : {
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"deploymentId" : 240000008
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{
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Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice_v3.cxs
Opened 251124_postprocess_cropped.mrc as #1, grid size 130,121,58, pixel
4.34,4.34,4.34, shown at level 0.0305, step 1, values float32
Opened 251124_postprocess_cropped_INM.mrc as #3, grid size 130,121,27, pixel
4.34,4.34,4.34, shown at level 0.0626, step 1, values float32
Opened 251124_postprocess_cropped_ONM_membraneOnly.mrc as #4, grid size
130,121,14, pixel 4.34,4.34,4.34, shown at level 0.0661, step 1, values
float32
Opened 251124_postprocess_cropped_ONM.mrc as #5, grid size 78,84,35, pixel
4.34,4.34,4.34, shown at level 0.074, step 1, values float32
Opened 251124_postprocess_cropped_INM.mrc as #6, grid size 130,121,27, pixel
4.34,4.34,4.34, shown at level 0.0879, step 1, values float32
Showing 251124_postprocess_cropped_v3_for_inm.seg - 4 regions, 4 surfaces
Log from Mon Nov 24 18:03:54 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice_v2.cxs
Opened 251124_postprocess_cropped.mrc as #1, grid size 130,121,58, pixel
4.34,4.34,4.34, shown at level 0.0533, step 1, values float32
Opened 251124_postprocess_cropped_INM.mrc as #3, grid size 130,121,27, pixel
4.34,4.34,4.34, shown at level 0.0626, step 1, values float32
Opened 251124_postprocess_cropped_ONM_membraneOnly.mrc as #4, grid size
130,121,14, pixel 4.34,4.34,4.34, shown at level 0.0661, step 1, values
float32
Opened 251124_postprocess_cropped_ONM.mrc as #5, grid size 78,84,35, pixel
4.34,4.34,4.34, shown at level 0.074, step 1, values float32
Opened 251124_postprocess_cropped_INM.mrc as #6, grid size 130,121,27, pixel
4.34,4.34,4.34, shown at level 0.0879, step 1, values float32
Log from Mon Nov 24 17:14:09 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/Mocki004/OneDrive - Universiteit
> Utrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_v1.seg"
> format segger
Summary of feedback from opening /Users/Mocki004/OneDrive - Universiteit
Utrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_v1.seg
---
notes | Opened 251124_postprocess_cropped.mrc as #1, grid size 130,121,58, pixel 4.34,4.34,4.34, shown at level 0.112, step 1, values float32
Only showing 60 of 76 regions.
Showing 60 of 76 region surfaces
Opened 251124_postprocess_cropped_v1.seg
Showing 251124_postprocess_cropped_v1.seg - 76 regions, 60 surfaces
> select #2.2
1 model selected
> select #2.1
1 model selected
> select add #2.2
2 models selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> select #2.25
1 model selected
Ungrouped to 12 regions, but did not show all surfaces, see Options
> select #2.1
1 model selected
> select subtract #2.1
Nothing selected
> select add #2.2
1 model selected
> select clear
> select add #2.1
1 model selected
> select add #2.2
2 models selected
> select #2.32
1 model selected
Ungrouped to 10 regions, but did not show all surfaces, see Options
> select #2.3
1 model selected
> close #2
> close #1
> open /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped.mrc
Opened 251124_postprocess_cropped.mrc as #1, grid size 130,121,58, pixel
4.34,4.34,4.34, shown at level 0.112, step 1, values float32
> volume #1 level 0.09183
> volume #1 level 0.06729
> open /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_v1.seg
Summary of feedback from opening
/Users/Mocki004/Library/CloudStorage/OneDrive-
UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_v1.seg
---
notes | Only showing 60 of 76 regions.
Showing 60 of 76 region surfaces
Opened 251124_postprocess_cropped_v1.seg
Showing 251124_postprocess_cropped_v1.seg - 76 regions, 60 surfaces
Map 251124_postprocess_cropped.mrc is now associated with
251124_postprocess_cropped_v1.seg
> select #2.2
1 model selected
> select add #2.1
2 models selected
> hide #!1 models
> select add #2.26
3 models selected
> select #2.26
1 model selected
> select clear
> select #2.26
1 model selected
Ungrouped to 12 regions, but did not show all surfaces, see Options
Drag select of 4453, 4441, 17506 of 18296 triangles, 4469, 18726 of 18760
triangles, 4420, 4423, 4404, 4408, 4411, 4407, 4425, 4485, 15528 of 15876
triangles, 4462, 13005 of 13460 triangles, 4412, 4445, 12858 of 13128
triangles, 4418, 4421, 4414, 4448, 4426, 9749 of 9852 triangles, 4409, 4450,
4422, 4479, 4456, 4419, 4413, 4455, 4435, 4434, 4492, 4478, 4493, 4457, 4537,
4543, 4522, 4470, 4477, 4416, 4454, 6092 of 6192 triangles, 4535, 4433, 4466,
4500, 4541, 4403, 3544, 4440, 4444, 4459, 4548, 4160 of 4408 triangles, 4555,
4562, 3573, 4486, 4468, 4446, 1976, 2126
> close #2
Segmenting 251124_postprocess_cropped.mrc, density threshold 0.067289
Showing 318 region surfaces
2735 watershed regions, grouped to 318 regions
Showing 251124_postprocess_cropped.seg - 318 regions, 318 surfaces
> close #2
> show #!1 models
> volume #1 level 0.02075
Segmenting 251124_postprocess_cropped.mrc, density threshold 0.020753
Showing 324 region surfaces
3543 watershed regions, grouped to 324 regions
Showing 251124_postprocess_cropped.seg - 324 regions, 324 surfaces
> close #2
Segmenting 251124_postprocess_cropped.mrc, density threshold 0.020753
Showing 1460 region surfaces
3543 watershed regions, grouped to 1460 regions
Showing 251124_postprocess_cropped.seg - 1460 regions, 1460 surfaces
Drag select of 3878, 3555, 3606, 3758, 3714, 3672, 3748, 3777, 3648, 3679,
3923, 3596, 3687, 3625, 3574, 3994, 3984, 3930, 3992, 4041, 3728, 3948, 3903,
3910, 3613, 3667, 3933, 3890, 3694, 3960, 4001, 3705, 4060, 3966, 3599, 4034,
3721, 3616, 3730, 3771, 3699, 3553, 4026, 3591, 3783, 3583, 3551, 3608, 3973,
3754, 4057, 3755, 3989, 3913, 3952, 4102, 3756, 3891, 4167, 4335, 3944, 3882,
4031, 4371, 4272, 4020, 3632, 3919, 3914, 3586, 3791, 3712, 4032, 3593, 4230,
3953, 3569, 3926, 4105, 4213, 4097, 4245, 3906, 3576, 3618, 3692, 3619, 3988,
3731, 3674, 3597, 3683, 4010, 4337, 4226, 3701, 3782, 3662, 3729, 3990, 3612,
3738, 4168, 4361, 3670, 3645, 4022, 3559, 3715, 3959, 3663, 3717, 4297, 3634,
3546, 3876, 4184, 4007, 4195, 4074, 3752, 3765, 3544, 3879, 3561, 4176, 3702,
3631, 3931, 3708, 3604, 3941, 4239, 3581, 4053, 4104, 3659, 4196, 4185, 3978,
3706, 4027, 4252, 3614, 3626, 3684, 4058, 3650, 4333, 4217, 3963, 3774, 4256,
3980, 3594, 3981, 3624, 4260, 4278, 3880, 3736, 3637, 3658, 3629, 4175, 3993,
3552, 4255, 3723, 3710, 4339, 4193, 4232, 4247, 4094, 3563, 4279, 3950, 3787,
3957, 4266, 4183, 1967, 3784, 3762, 4181, 4125, 4017, 3972, 3894, 4113, 4140,
4194, 4276, 1892, 3685, 4262, 4359, 4066, 3642, 2055, 3643, 4093, 3996, 3925,
4037, 4014, 3570, 4231, 3789, 1880, 2496, 4253, 2013, 4379, 4200, 3666, 4396,
3954, 4263, 3572, 3899, 3743, 4221, 3579, 4038, 3928, 4267, 3652, 3602, 2432,
4227, 2031, 1743, 1750, 3665, 4108, 2584, 3605, 3725, 4071, 4248, 3577, 4318,
4164, 3716, 1964, 4240, 2176, 3565, 4003, 3567, 4199, 4271, 4013, 3719, 3575,
3653, 1850, 3759, 4219, 4206, 4201, 4212, 4111, 4273, 4207, 4249, 3556, 4223,
4236, 4086, 3628, 3560, 3746, 4077, 3740, 4258, 3778, 3654, 3975, 4202, 3986,
3623, 4315, 4265, 3733, 2095, 3698, 3609, 3936, 4163, 4171, 4268, 4191, 3668,
3749, 4269, 2805, 3793, 3700, 4257, 3646, 3924, 3887, 3566, 3921, 3915, 2469,
4189, 3779, 4246, 3681, 3588, 4205, 2467, 1908, 3557, 4323, 1832, 2447, 2358,
1768, 3638, 1909, 1907, 3693, 3639, 4370, 4238, 4179, 3601, 4320, 1796, 4079,
1899, 4287, 4173, 4325, 4000, 4234, 3945, 4169, 4215, 2515, 2359, 4044, 2021,
2458, 4204, 1857, 3885, 4404, 3641, 3589, 3033, 3907, 2199, 3178, 2209, 3745,
3911, 3620, 4229, 3937, 1881, 3293, 3892, 3363, 4174, 4338, 2041, 3792, 3897,
1820, 3337, 4241, 4233, 2109, 2213, 4182, 3962, 3200, 1771, 1769, 3935, 2060,
3768, 3309, 3883, 3763, 3949, 2105, 2186, 2926, 3977, 2086, 2063, 3390, 4218,
4259, 4188, 3355, 2519, 3564, 1871, 4186, 4192, 3118, 4270, 2371, 2023, 3688,
1845, 2141, 3580, 3545, 3956, 2152, 3384, 3107, 4225, 3098, 4264, 2377, 3324,
3655, 2208, 3095, 2131, 3364, 3964, 1930, 2454, 3794, 1889, 3908, 2170, 2497,
3901, 3554, 4250, 4180, 2142, 2343, 3895, 3772, 4275, 4187, 3305, 2066, 4224,
4214, 2101, 2891, 3063, 1971, 3750, 3742, 3677, 3053, 2957, 2221, 3185, 3075,
3029, 3587, 4211, 4203, 4394, 3673, 2518, 3697, 2215, 3164, 1830, 4080, 2167,
2937, 3015, 3886, 2535, 3775, 3739, 1833, 3695, 2405, 2183, 2642, 2293, 4243,
4237, 3103, 2973, 3713, 4178, 3338, 1929, 2181, 2230, 4210, 4045, 1989, 2168,
3584, 4222, 4165, 2978, 2495, 4235, 4190, 3040, 2531, 4261, 2410, 1730, 2146,
3278, 2471, 3747, 3302, 3934, 4277, 2303, 3230, 2439, 4228, 1914, 4244, 3090,
2745, 3766, 4274, 4382, 4254, 4242, 2189, 2453, 3720, 4048, 2503, 4170, 2461,
2929, 4172, 3969, 2885, 4198, 3039, 2162, 2734, 2455, 4368, 2867, 2485, 2930,
3078, 3283, 1987, 2969, 2443, 2357, 3770, 2349, 3306, 3215, 3110, 2370, 3304,
3295, 3233, 3026, 3006, 3004, 2834, 4109, 3317, 2952, 2295, 3622, 3170, 3333,
2404, 2334, 2457, 3656, 3193, 3146, 4209, 3690, 2927, 2329, 3301, 2951, 2800,
2790, 2024, 3349, 3610, 2525, 2592, 3196, 3120, 3268, 2419, 3145, 2886, 2835,
2323, 3223, 2558, 2463, 3186, 2361, 2057, 4220, 2875, 2833, 2321, 3649, 4251,
3334, 2756, 1958, 2968, 2742, 2435, 2600, 3071, 3062, 2958, 3101, 2594, 3927,
4166, 2402, 2318, 3330, 2997, 2904, 4197, 2863, 3660, 3548, 2416, 3229, 3140,
3125, 2945, 2424, 2407, 2761, 3114, 3205, 2501, 4177, 3292, 2950, 3339, 2773,
2124, 2426, 3041, 3222, 2278, 2688, 2783, 3176, 3381, 2583, 3195, 3323, 3060,
4216, 3377, 2473, 2438, 3513, 3259, 3469, 3181, 3087, 3262, 3154, 2038, 2522,
2588, 3284, 2483, 2480, 3188, 4208, 3388, 2812, 2779, 2472, 3509, 3093, 3238,
3097, 3081, 2602, 3050, 3335, 2818, 3391, 2631, 2816, 2762, 3490, 3382, 3054,
3100, 3311, 1807, 3331, 3070, 3279, 3031, 3493, 3066, 3197, 2574, 2710, 3109,
2556, 2500, 3166, 2557, 3162, 3313, 3464, 3124, 2609, 3174, 2827, 3139, 3157,
3444, 3280, 2943, 2949, 2581, 2807, 3483, 2924, 2757, 3486, 2963, 3231, 3254,
3220, 3128, 3251, 2822, 3149, 2712, 1 251124_postprocess_cropped.mrc
> hide #!1 models
> set bgColor gray
> lighting soft
> graphics silhouettes true
> select #2.265
1 model selected
> select add #2.526
2 models selected
> select add #2.648
3 models selected
> select add #2.224
4 models selected
> select add #2.668
5 models selected
> select add #2.48
6 models selected
> select add #2.44
7 models selected
> select subtract #2.48
6 models selected
> select subtract #2.44
5 models selected
> select add #2.40
6 models selected
> select add #2.926
7 models selected
> select add #2.660
8 models selected
> select add #2.601
9 models selected
> select subtract #2.926
8 models selected
> select add #2.926
9 models selected
> select add #2.1455
10 models selected
> select add #2.417
11 models selected
> select add #2.525
12 models selected
> select add #2.359
13 models selected
> select add #2.271
14 models selected
> select add #2.638
15 models selected
> select add #2.809
16 models selected
> select add #2.324
17 models selected
> select add #2.676
18 models selected
> select add #2.457
19 models selected
> select add #2.325
20 models selected
> select add #2.94
21 models selected
> select add #2.258
22 models selected
> select add #2.1032
23 models selected
> select add #2.111
24 models selected
> select add #2.431
25 models selected
> select add #2.376
26 models selected
> select add #2.804
27 models selected
> select add #2.908
28 models selected
> select add #2.584
29 models selected
> select add #2.350
30 models selected
> select add #2.424
31 models selected
> select add #2.302
32 models selected
> select add #2.409
33 models selected
> select add #2.369
34 models selected
> select add #2.413
35 models selected
> select add #2.580
36 models selected
> select add #2.195
37 models selected
> select add #2.519
38 models selected
> select add #2.398
39 models selected
> select add #2.449
40 models selected
> select add #2.944
41 models selected
> select add #2.817
42 models selected
> select add #2.202
43 models selected
> select add #2.200
44 models selected
> select add #2.243
45 models selected
> select add #2.313
46 models selected
> select add #2.490
47 models selected
> select add #2.269
48 models selected
> select add #2.381
49 models selected
> select add #2.1120
50 models selected
> select add #2.1101
51 models selected
> select add #2.596
52 models selected
> select add #2.214
53 models selected
> select add #2.542
54 models selected
> select add #2.372
55 models selected
> select add #2.485
56 models selected
> select add #2.569
57 models selected
> select add #2.1015
58 models selected
> select add #2.439
59 models selected
> select add #2.860
60 models selected
> select add #2.1077
61 models selected
> select add #2.321
62 models selected
> select add #2.501
63 models selected
> select add #2.511
64 models selected
> select add #2.403
65 models selected
> select add #2.772
66 models selected
> select add #2.738
67 models selected
> select add #2.428
68 models selected
> select add #2.401
69 models selected
> select add #2.491
70 models selected
> select add #2.451
71 models selected
> select add #2.133
72 models selected
> select add #2.353
73 models selected
> select add #2.1033
74 models selected
> select add #2.764
75 models selected
> select add #2.502
76 models selected
> select add #2.352
77 models selected
> select add #2.747
78 models selected
> select add #2.903
79 models selected
> select add #2.996
80 models selected
> select add #2.113
81 models selected
> select add #2.630
82 models selected
> select add #2.470
83 models selected
> select add #2.180
84 models selected
> select add #2.825
85 models selected
> select add #2.343
86 models selected
> select add #2.484
87 models selected
> select add #2.452
88 models selected
> select add #2.296
89 models selected
> select add #2.637
90 models selected
> select add #2.463
91 models selected
> select add #2.11
92 models selected
> select subtract #2.11
91 models selected
Grouped 91 regions
> select #2.11
1 model selected
Ungrouped to 13 regions
> select #2.631
1 model selected
> select add #2.410
2 models selected
> select add #2.643
3 models selected
> select add #2.1193
4 models selected
> select add #2.40
5 models selected
Grouped 5 regions
> select add #2.94
2 models selected
> select add #2.258
3 models selected
> select add #2.195
4 models selected
> select add #2.224
5 models selected
> select add #2.265
6 models selected
> select add #2.200
7 models selected
> select add #2.243
8 models selected
> select add #2.100
9 models selected
Grouped 9 regions
> select #2.489
1 model selected
Ungrouped to 4 regions
> select #2.48
1 model selected
Ungrouped to 6 regions
> select #2.44
1 model selected
> select add #2.7
2 models selected
Ungrouped to 16 regions
> select #2.321
1 model selected
> select add #2.302
2 models selected
> select add #2.269
3 models selected
> select add #2.11
4 models selected
> select add #2.195
5 models selected
> select add #2.100
6 models selected
> select add #2.40
7 models selected
> select add #2.94
8 models selected
> select add #2.177
9 models selected
> select subtract #2.177
8 models selected
> select add #2.575
9 models selected
> select add #2.177
10 models selected
Grouped 10 regions
> select #2.41
1 model selected
Ungrouped to 8 regions
> select #2.24
1 model selected
Ungrouped to 12 regions
> select #2.381
1 model selected
> select add #2.424
2 models selected
> select add #2.410
3 models selected
> select add #2.7
4 models selected
Grouped 4 regions
> select #2.269
1 model selected
> select add #2.44
2 models selected
> select add #2.7
3 models selected
Grouped 3 regions
> select clear
> select #2.7
1 model selected
> select clear
[Repeated 1 time(s)]Drag select of 3790, 3848, 3804, 3558, 3718, 3627, 3802,
3773, 3872, 3732, 3704, 3647, 3849, 3607, 3832, 3798, 3547, 3862, 3707, 3871,
3744, 3829, 4036, 3753, 4121, 3621, 3808, 3828, 3726, 4344, 3820, 3711, 3869,
3722, 3833, 4124, 3870, 3861, 3826, 4340, 4122, 3796, 3856, 3853, 3836, 3838,
3983, 3549, 3696, 3592, 3800, 3617, 3835, 3795, 4311, 3615, 3830, 3955, 3675,
4293, 4352, 3803, 3839, 4119, 4126, 3840, 3864, 4116, 4341, 3815, 1292, 3761,
3724, 3664, 1115, 978, 3785, 3757, 3611, 3635, 3598, 4304, 1244, 3841, 4347,
4015, 4307, 1383, 3852, 4123, 3873, 4115, 3821, 4016, 4292, 3805, 3562, 4295,
4342, 3633, 3767, 4096, 3843, 4280, 3801, 3865, 4314, 4129, 1070, 4134, 4281,
3929, 3568, 4091, 3578, 1008, 3834, 1151, 3985, 3855, 1020, 1102, 4345, 3943,
4135, 3974, 3550, 3797, 3788, 4156, 1271, 4004, 3776, 3764, 4291, 951, 1296,
4118, 3858, 4374, 4321, 3965, 4348, 4343, 4099, 1124, 4137, 4322, 4328, 4049,
4282, 3898, 4133, 3987, 3769, 4101, 4087, 3780, 4296, 4385, 1076, 4381, 3735,
3585, 4035, 4351, 4072, 3900, 3582, 3727, 3680, 4286, 3678, 4306, 4067, 3998,
3940, 3893, 3970, 4312, 3760, 4141, 4305, 3817, 3573, 3909, 3867, 3737, 4300,
3671, 4136, 4029, 4313, 3967, 3896, 516, 470, 4068, 3881, 3741, 4301, 4021,
3938, 3902, 3651, 3751, 3600, 4294, 3918, 3850, 4289, 4142, 3951, 3851, 4078,
3669, 4143, 4362, 3823, 3686, 4061, 984, 4023, 4006, 3824, 3603, 3822, 4330,
4324, 3859, 3781, 3917, 4085, 3961, 3946, 4043, 3847, 4349, 4284, 4040, 955,
3874, 3825, 1213, 3644, 3689, 3636, 4002, 3857, 3814, 3958, 4283, 4051, 4030,
3888, 4298, 3922, 3657, 3571, 3905, 4098, 967, 3916, 3912, 4288, 3997, 4161,
4389, 3920, 290, 3866, 3590, 4107, 3806, 3995, 4131, 3816, 1019, 4081, 1154,
4326, 4117, 3846, 3947, 3982, 3860, 3889, 3682, 3661, 4392, 4373, 4299, 4024,
3734, 3968, 3831, 3904, 1191, 553, 220, 4084, 4354, 4319, 1205, 275, 1133,
4005, 3979, 4144, 4148, 4008, 3837, 1087, 3845, 4353, 4316, 3877, 216, 116,
3786, 992, 4332, 3854, 3691, 677, 4336, 4302, 4309, 4303, 1471, 3991, 4372,
1168, 74, 109, 447, 4308, 4069, 4120, 4050, 3863, 4386, 4317, 3942, 6, 4327,
942, 4114, 3810, 3807, 690, 4025, 3932, 91, 190, 939, 604, 876, 4399, 1211,
560, 4331, 300, 4062, 1533, 4059, 3939, 3827, 289, 527, 3630, 3813, 4334,
4132, 4011, 306, 1129, 3976, 436, 3640, 349, 425, 922, 4106, 1085, 4310, 4138,
4391, 3809, 4329, 4139, 199, 446, 551, 4056, 233, 171, 472, 183, 107, 3819,
4042, 4127, 315, 698, 274, 889, 4046, 159, 451, 3875, 88, 3818, 4128, 11,
3971, 580, 3999, 217, 646, 3812, 3811, 488, 653, 578, 947, 4012, 4054, 1122,
288, 882, 123, 574, 3844, 31, 4290, 376, 4158, 599, 1007, 905, 405, 105, 4384,
178, 4285, 352, 302, 4346, 369, 4377, 265, 813, 420, 1099, 49, 4092, 594, 225,
528, 93, 875, 4028, 1045, 4, 39, 203, 4146, 307, 4395, 4364, 442, 169, 4155,
160, 128, 3868, 695, 140, 170, 500, 114, 4365, 499, 4089, 4039, 111, 4112,
529, 167, 898, 378, 1084, 505, 1159, 1153, 519, 492, 360, 570, 1039, 239, 428,
539, 545, 865, 870, 1262, 427, 655, 798, 791, 654, 172, 512, 150, 162, 644,
579, 945, 384, 598, 89, 99, 634, 75, 213, 546, 318, 525, 230, 617, 871, 21,
244, 221, 506, 603, 104, 444, 517, 787, 548, 383, 786, 732, 332, 422, 701,
686, 466, 261, 228, 1218, 595, 254, 149, 60, 321, 342, 186, 685, 267, 630,
635, 557, 730, 80, 143, 613, 689, 373, 819, 211, 959, 729, 354, 287, 761, 751,
760, 445, 490, 549, 757, 212, 825, 408, 480, 9, 744, 353, 583, 52, 1330, 1183,
1523, 684, 949, 961, 974, 979, 1233, 1223, 1112, 1114, 1118, 911, 1391, 844,
581, 558, 1503, 783, 848, 639, 622, 621, 610, 1405, 776, 777, 779, 1107, 1111,
1123, 1130, 908, 1482, 915, 828, 861, 1422, 1426, 1486, 1504, 1413, 1416
Grouped 638 regions
> select clear
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice.cxs
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_v2.seg
> models #2
> select clear
> select #2.1
1 model selected
> select add #2.7
2 models selected
> select clear
> select add #2.80
1 model selected
> select add #2.203
2 models selected
> select add #2.28
3 models selected
> select add #2.175
4 models selected
> select add #2.35
5 models selected
> select add #2.196
6 models selected
> select add #2.158
7 models selected
> select add #2.91
8 models selected
> select add #2.482
9 models selected
> select subtract #2.158
8 models selected
> select add #2.32
9 models selected
> select add #2.154
10 models selected
> select subtract #2.154
9 models selected
> select add #2.188
10 models selected
> select add #2.71
11 models selected
> select add #2.488
12 models selected
> select add #2.1224
13 models selected
> select add #2.270
14 models selected
> select add #2.378
15 models selected
> select add #2.528
16 models selected
> select add #2.190
17 models selected
> select subtract #2.190
16 models selected
> select add #2.377
17 models selected
> select add #2.17
18 models selected
> select add #2.29
19 models selected
> select subtract #2.29
18 models selected
Grouped 18 regions
> select #2.38
1 model selected
Ungrouped to 5 regions
> select #2.154
1 model selected
Ungrouped to 4 regions
> select #2.307
1 model selected
> select add #2.2
2 models selected
> select add #2.12
3 models selected
> select add #2.28
4 models selected
Grouped 4 regions
> select #2.370
1 model selected
Ungrouped to 3 regions
> select #2.28
1 model selected
> select add #2.2
2 models selected
> select add #2.158
3 models selected
> select #2.158
1 model selected
Ungrouped to 4 regions
> select #2.29
1 model selected
Ungrouped to 6 regions
> select #2.715
1 model selected
Ungrouped to 2 regions
> select #2.190
1 model selected
Ungrouped to 4 regions
> select #2.9
1 model selected
Ungrouped to 11 regions
> select #2.16
1 model selected
Ungrouped to 9 regions
> select #2.90
1 model selected
Ungrouped to 4 regions
> select #2.16
1 model selected
> select add #2.977
2 models selected
> select add #2.107
3 models selected
> select add #2.80
4 models selected
> select add #2.100
5 models selected
> select add #2.78
6 models selected
> select add #2.2
7 models selected
> select add #2.48
8 models selected
> select add #2.65
9 models selected
> select add #2.66
10 models selected
> select add #2.28
11 models selected
Grouped 11 regions
> select #2.40
1 model selected
> select add #2.2
2 models selected
Grouped 2 regions
> select #2.276
1 model selected
> select add #2.1365
2 models selected
> select add #2.2
3 models selected
Grouped 3 regions
> select #2.740
1 model selected
> select #2.36
1 model selected
Ungrouped to 6 regions
> select #2.16
1 model selected
> select add #2.740
2 models selected
> select add #2.2
3 models selected
Grouped 3 regions
> select #2.3
1 model selected
Ungrouped to 11 regions
> select #2.80
1 model selected
> select add #2.78
2 models selected
> select add #2.36
3 models selected
> select add #2.2
4 models selected
Grouped 4 regions
> select #2.211
1 model selected
> select add #2.456
2 models selected
> select add #2.400
3 models selected
> select #2.10
1 model selected
> select add #2.105
2 models selected
> select add #2.104
3 models selected
> select add #2.237
4 models selected
> select add #2.362
5 models selected
> select add #2.774
6 models selected
> select add #2.408
7 models selected
> select subtract #2.408
6 models selected
> select subtract #2.237
5 models selected
Grouped 5 regions
> select #2.237
1 model selected
Ungrouped to 2 regions
> select #2.10
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> select #2.408
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> select add #2.26
2 models selected
> select add #2.2
3 models selected
Grouped 3 regions
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice.cxs
> select #2.21
1 model selected
Ungrouped to 7 regions
> select #2.104
1 model selected
> select add #2.80
2 models selected
Grouped 2 regions
> select #2.527
1 model selected
> select add #2.21
2 models selected
> select add #2.69
3 models selected
> select #2.69
1 model selected
Ungrouped to 5 regions
> select #2.80
1 model selected
> select add #2.133
2 models selected
> select add #2.21
3 models selected
> select add #2.527
4 models selected
> select add #2.210
5 models selected
> select add #2.763
6 models selected
Grouped 6 regions
> select add #2.2
2 models selected
Grouped 2 regions
> select add #2.659
2 models selected
> select add #2.948
3 models selected
Grouped 3 regions
> select add #2.27
2 models selected
> select #2.27
1 model selected
Ungrouped to 5 regions
> select #2.21
1 model selected
Ungrouped to 0 regions
> select add #2.80
1 model selected
> select add #2.21
2 models selected
> select add #2.2
3 models selected
Grouped 3 regions
> select #2.211
1 model selected
> select add #2.456
2 models selected
> select #2.456
1 model selected
Ungrouped to 3 regions
> select #2.21
1 model selected
> select add #2.211
2 models selected
> select add #2.442
3 models selected
> select add #2.520
4 models selected
> select add #2.847
5 models selected
> select add #2.771
6 models selected
> select add #2.400
7 models selected
Grouped 7 regions
Ungrouped to 7 regions
> select #2.151
1 model selected
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #2.154
1 model selected
Ungrouped to 0 regions
> select #2.144
1 model selected
Ungrouped to 0 regions
> select #2.144
1 model selected
> select add #2.138
2 models selected
> select add #2.153
3 models selected
> select add #2.141
4 models selected
> select add #2.142
5 models selected
> select add #2.19
6 models selected
> select add #2.154
7 models selected
> select add #2.149
8 models selected
> select add #2.2
9 models selected
Grouped 9 regions
> select #2.31
1 model selected
Ungrouped to 5 regions
> select #2.138
1 model selected
Ungrouped to 0 regions
> select #2.79
1 model selected
> select #2.19
1 model selected
> select #2.138
1 model selected
> select #2.315
1 model selected
> select #2.79
1 model selected
> select add #2.138
2 models selected
> select add #2.19
3 models selected
> select add #2.315
4 models selected
> select add #2.340
5 models selected
> select add #2.109
6 models selected
> select add #2.454
7 models selected
> select add #2.438
8 models selected
> select add #2.664
9 models selected
> select subtract #2.340
8 models selected
> select add #2.340
9 models selected
> select add #2.53
10 models selected
> select add #2.562
11 models selected
> select add #2.2
12 models selected
> select add #2.29
13 models selected
Grouped 13 regions
> select #2.77
1 model selected
Ungrouped to 6 regions
> select #2.68
1 model selected
Ungrouped to 3 regions
> select subtract #2.77
2 models selected
> select add #2.53
3 models selected
> select #2.61
1 model selected
Ungrouped to 5 regions
> select #2.151
1 model selected
Ungrouped to 0 regions
> select #2.151
1 model selected
> select add #2.53
2 models selected
> select add #2.178
3 models selected
> select subtract #2.178
2 models selected
> select subtract #2.151
1 model selected
> select add #2.178
2 models selected
> select add #2.77
3 models selected
> select add #2.844
4 models selected
> select add #2.67
5 models selected
> select add #2.2
6 models selected
Grouped 6 regions
> select add #2.458
2 models selected
> select add #2.540
3 models selected
> select add #2.468
4 models selected
Grouped 4 regions
> select add #2.815
2 models selected
Grouped 2 regions
> select #2.75
1 model selected
Ungrouped to 6 regions
> select #2.61
1 model selected
> select add #2.67
2 models selected
> select add #2.461
3 models selected
> select add #2.666
4 models selected
> select add #2.654
5 models selected
> select add #2.363
6 models selected
> select add #2.129
7 models selected
> select add #2.314
8 models selected
> select add #2.2
9 models selected
Grouped 9 regions
> select add #2.757
2 models selected
> select add #2.13
3 models selected
> select add #2.147
4 models selected
> select add #2.364
5 models selected
> select add #2.684
6 models selected
> select add #2.1133
7 models selected
> select add #2.586
8 models selected
Grouped 8 regions
> select add #2.112
2 models selected
> select #2.112
1 model selected
Ungrouped to 3 regions
> select #2.18
1 model selected
Ungrouped to 8 regions
> select #2.112
1 model selected
> select add #2.75
2 models selected
> select add #2.13
3 models selected
> select add #2.2
4 models selected
Grouped 4 regions
> select subtract #2.2
Nothing selected
> select #2.1216
1 model selected
> select add #2.2
2 models selected
Grouped 2 regions
> select #2.151
1 model selected
> select #2.145
1 model selected
> select add #2.2
2 models selected
Grouped 2 regions
> select clear
Drag select of 3555, 3606, 3758, 3777, 3648, 3625, 3994, 3984, 3948, 3613,
3667, 3694, 4001, 3705, 4060, 3966, 3599, 4034, 3616, 3730, 3771, 3699, 4026,
3591, 3608, 3754, 4057, 4102, 3756, 3891, 4167, 4335, 4031, 4371, 4272, 4020,
3632, 3919, 3914, 3586, 3791, 4032, 4230, 3953, 3569, 3926, 4105, 4213, 4097,
4245, 3576, 3618, 3692, 3619, 3988, 3731, 3674, 3683, 4337, 4226, 3701, 3662,
3990, 3612, 3738, 4168, 4361, 3670, 3645, 3715, 3663, 4297, 3634, 3546, 4184,
4195, 4074, 3752, 3765, 3561, 4176, 3702, 3631, 3708, 3604, 3941, 4239, 3581,
4053, 4104, 3659, 4196, 4185, 3706, 4252, 3614, 3626, 3684, 4058, 3650, 4333,
4217, 3963, 3774, 4256, 3594, 3981, 3624, 4260, 3736, 3637, 3658, 3629, 4175,
3993, 3552, 4255, 3710, 4339, 4193, 4232, 4247, 4094, 3563, 4279, 4266, 4183,
1967, 3784, 4181, 4125, 3894, 4113, 4140, 4194, 4276, 3685, 4262, 4359, 3642,
2055, 3643, 4093, 3996, 3925, 4037, 4014, 3570, 4231, 3789, 2496, 4253, 4379,
4200, 3666, 4396, 3743, 4221, 4038, 3928, 4267, 3652, 3602, 2432, 4227, 2031,
3665, 4108, 2584, 3605, 3725, 4071, 4248, 3577, 4318, 4164, 1964, 4240, 2176,
3567, 4199, 4271, 4013, 3719, 3575, 3653, 3759, 4219, 4206, 4201, 4212, 4111,
4273, 4207, 4249, 3556, 4223, 4236, 3628, 3560, 3746, 4077, 3740, 4258, 3778,
3654, 3975, 4202, 3986, 3623, 4315, 4265, 2095, 3698, 3609, 3936, 4163, 4171,
4268, 4191, 3668, 3749, 4269, 2805, 3793, 3700, 4257, 3646, 3924, 3887, 3566,
3921, 3915, 2469, 4189, 3779, 4246, 3681, 3588, 4205, 2467, 3557, 4323, 2447,
2358, 3638, 1907, 3693, 3639, 4370, 4238, 4179, 3601, 4320, 4079, 1899, 4287,
4173, 4325, 4000, 4234, 3945, 4169, 4215, 2515, 2359, 4044, 2021, 2458, 4204,
1857, 4404, 3641, 3589, 3033, 3907, 2199, 3178, 2209, 3745, 3911, 3620, 4229,
3937, 1881, 3293, 3363, 4174, 4338, 2041, 3792, 3897, 3337, 4241, 4233, 2109,
2213, 3962, 3200, 3935, 2060, 3768, 3309, 3883, 3763, 3949, 2105, 2186, 2926,
3977, 2086, 2063, 3390, 4218, 4259, 4188, 3355, 2519, 3564, 1871, 4186, 4192,
3118, 4270, 2371, 2023, 3688, 2141, 3580, 3545, 3956, 2152, 3384, 3107, 4225,
3098, 4264, 2377, 3324, 3655, 2208, 3095, 2131, 3364, 3964, 2454, 3794, 3908,
2170, 2497, 3901, 3554, 4250, 4180, 2142, 2343, 3895, 3772, 4275, 4187, 3305,
2066, 4224, 4214, 2101, 2891, 3063, 1971, 3750, 3742, 3677, 3053, 2957, 2221,
3185, 3075, 3029, 3587, 4211, 4203, 4394, 3673, 2518, 3697, 2215, 3164, 1830,
4080, 2167, 2937, 3015, 3886, 2535, 3775, 3739, 1833, 3695, 2405, 2183, 2642,
2293, 4243, 4237, 3103, 2973, 3713, 4178, 3338, 2181, 2230, 4210, 4045, 1989,
2168, 3584, 4222, 4165, 2978, 2495, 4235, 4190, 3040, 2531, 4261, 2410, 2146,
3278, 2471, 3747, 3302, 3934, 4277, 2303, 3230, 2439, 4228, 1914, 4244, 3090,
2745, 3766, 4274, 4382, 4254, 4242, 2189, 2453, 3720, 4048, 2503, 4170, 2461,
2929, 4172, 3969, 2885, 4198, 3039, 2162, 2734, 2455, 4368, 2867, 2485, 2930,
3078, 3283, 1987, 2969, 2443, 2357, 3770, 2349, 3306, 3215, 3110, 2370, 3304,
3295, 3233, 3026, 3006, 3004, 2834, 4109, 3317, 2952, 2295, 3622, 3170, 3333,
2404, 2334, 2457, 3656, 3193, 3146, 4209, 3690, 2927, 2329, 3301, 2951, 2800,
2790, 3349, 3610, 2525, 2592, 3196, 3120, 3268, 2419, 3145, 2886, 2835, 2323,
3223, 2558, 2463, 3186, 2361, 2057, 4220, 2875, 2833, 2321, 3649, 4251, 3334,
2756, 1958, 2968, 2742, 2435, 2600, 3071, 3062, 2958, 3101, 2594, 3927, 2402,
2318, 3330, 2997, 2904, 2863, 3660, 3548, 2416, 3229, 3140, 3125, 2945, 2424,
2407, 2761, 3114, 3205, 2501, 4177, 3292, 2950, 3339, 2773, 2124, 2426, 3041,
3222, 2278, 2688, 2783, 3176, 3381, 2583, 3195, 3323, 3060, 4216, 3377, 2473,
2438, 3513, 3259, 3469, 3181, 3087, 3262, 3154, 2038, 2522, 2588, 3284, 2483,
2480, 3188, 4208, 3388, 2812, 2779, 2472, 3509, 3093, 3238, 3097, 3081, 2602,
3050, 3335, 2818, 3391, 2631, 2816, 2762, 3490, 3382, 3054, 3100, 3311, 3331,
3070, 3279, 3031, 3493, 3066, 3197, 2574, 2710, 3109, 2556, 2500, 3166, 2557,
3162, 3313, 3464, 3124, 2609, 3174, 2827, 3139, 3157, 3444, 3280, 2943, 2949,
2581, 2807, 3483, 2924, 2757, 3486, 2963, 3231, 3254, 3220, 3128, 3251, 2822,
3149, 2712, 2607, 2608, 2056, 2517, 2045, 2205, 2489, 2035, 2484, 2016, 2433,
2136, 2015, 2434, 2145, 2561, 2564, 2147, 2009, 2415, 2007, 2010, 2412, 2281,
2291, 2111, 2114, 2122, 2559, 1988, 1992, 1997, 2272, 2286, 2400, 2273, 2545,
2569, 2572, 2449, 2159, 2160, 2311, 2425, 2427, 2429, 1901, 2133, 2137, 2143,
2406, 1940, 2053, 2360, 2634, 2514, 2043, 2335, 2494, 2372, 2072, 2532, 2120,
2127, 2566, 2302, 2440, 2441, 2365, 2368, 2636, 2061, 2530, 2362, 2228, 1932,
1938, 2596, 2351, 2499, 2032, 2478, 2797, 2174, 2363, 2229, 1953, 1756, 2612,
2234, 2068, 2526
Grouped 754 regions
> select clear
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice.cxs
> select #2.7
1 model selected
> select add #2.2
2 models selected
Grouped 2 regions
> color #2.2 white
> color #2.1 #7faa99ff
> select #2.3
1 model selected
> color #2.3 #318d67ff
> select clear
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_v2.seg
> models #2
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice.cxs
> hide #!2 models
> show #!1 models
> volume #1 level 0.06729
> ui mousemode right clip
> open /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_INM.mrc
Opened 251124_postprocess_cropped_INM.mrc as #3, grid size 130,121,27, pixel
4.34,4.34,4.34, shown at level 0.113, step 1, values float32
> ui mousemode right "clip rotate"
> ui mousemode right clip
> hide #!3 models
> set bgColor white
> hide #2.3 models
> hide #2.2 models
> hide #2.1 models
> hide #!1 models
> show #!1 models
> color #1 #b3b3b3ff models
> color #1 white models
> color #1 #ffffff00 models
> volume #1 level 0.03937
> volume #1 level -0.06386
> show #!3 models
> hide #!3 models
> volume #1 level 0.05544
> hide #!1 models
> show #!3 models
> surface dust #3 size 43.4
> volume #3 level 0.08392
> color #3 #fafafaff models
> color #3 #318d67ff models
> show #!1 models
> ui mousemode right "crop volume"
> hide #!3 models
> volume #1 region 0,0,0,129,120,42
> volume #1 region 0,0,0,129,120,41
> volume #1 region 0,0,14,129,120,41
> surface dust #1 size 43.4
> open /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_ONM_membraneOnly.mrc
Opened 251124_postprocess_cropped_ONM_membraneOnly.mrc as #4, grid size
130,121,14, pixel 4.34,4.34,4.34, shown at level 0.1, step 1, values float32
> hide #!1 models
> volume #4 level 0.06606
> surface dust #4 size 43.4
> color #4 #7faa99ff models
> show #!1 models
> volume #1 level 0.07287
> color #1 white models
> hide #!4 models
> volume #1 region 0,0,13,129,120,41
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> volume #4 region 0,0,0,129,120,13
> open /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_ONM.mrc
Opened 251124_postprocess_cropped_ONM.mrc as #5, grid size 78,84,35, pixel
4.34,4.34,4.34, shown at level 0.124, step 1, values float32
> hide #!4 models
> volume #5 level 0.04262
> volume #5 level 0.04959
> surface dust #5 size 43.4
> volume #5 region 0,0,0,77,83,25
> ui mousemode right "crop volume"
> volume #!5 showOutlineBox true
> volume #5 region 0,0,0,77,83,14
> color #5 #7faa99ff models
> show #!1 models
> volume #1 region 0,0,13,129,120,27
> volume #1 region 0,0,7,129,120,34
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice.cxs
> volume #1 region 0,44,7,129,120,34
> volume #5 region 0,0,0,77,83,15
[Repeated 1 time(s)]
> volume #5 region 0,26,0,77,83,15
> volume #5 region 0,0,0,77,83,15
> hide #!5 models
> volume #1 region 0,44,15,129,120,34
> show #!5 models
> volume #5 region 0,28,0,77,83,15
> volume #5 region 0,29,0,77,83,15
[Repeated 1 time(s)]
> hide #!5 models
> volume #1 region 0,43,15,129,120,34
> volume #1 region 0,0,15,129,120,34
> show #!5 models
> volume #1 region 0,0,15,129,120,34
> hide #!1 models
> volume #5 region 0,0,0,77,83,15
> show #!1 models
> volume #1 region 0,0,15,129,120,15
> volume #1 region 0,0,15,129,120,38
> volume #1 region 0,0,15,129,120,34
> hide #!1 models
> volume #5 region 0,0,0,77,83,15
[Repeated 1 time(s)]
> show #!1 models
> select clear
> volume #!1,5 showOutlineBox false
> volume #!1,5 showOutlineBox true
> volume #!1,5 showOutlineBox false
> volume #1 level 0.06154
> ui mousemode right clip
> ui tool show "Side View"
> surface dust #1 size 43.4
> surface dust #5 size 43.4
> show #!2 models
> hide #!2 models
> show #!3 models
> open /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_INM.mrc
Opened 251124_postprocess_cropped_INM.mrc as #6, grid size 130,121,27, pixel
4.34,4.34,4.34, shown at level 0.113, step 1, values float32
> hide #!1 models
> hide #!3 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> volume #6 level 0.02072
> view
> volume #6 level 0.02072
> color #6 #318d67ff models
> color #6 #787878ff models
> color #6 white models
> ui mousemode right "crop volume"
> volume #6 region 0,0,0,129,120,9
> show #!3 models
> volume #3 region 0,0,0,129,120,26
[Repeated 1 time(s)]
> hide #!3 models
> volume #6 region 0,0,0,129,120,10
> show #!3 models
> hide #!6 models
> volume #3 region 0,0,0,129,120,26
> volume #3 region 0,0,1,129,120,26
> volume #3 level 0.07115
> volume #3 level 0.07415
> volume #3 region 0,0,8,129,120,26
> show #!6 models
> volume #6 level 0.05668
> volume #6 level 0.05286
> show #!5 models
> show #!1 models
> view orient
> turn x -90
> ui tool show "Side View"
> volume #3 level 0.08416
> volume #6 level 0.05439
> hide #!3 models
> hide #!6 models
> hide #!5 models
> view
[Repeated 1 time(s)]
> ui mousemode right "crop volume"
> volume #!1 showOutlineBox true
> volume #1 region 0,0,15,129,120,57
> volume #1 region 0,0,0,129,120,57
> view orient
> turn x -90
> ui tool show "Side View"
> volume #!1 showOutlineBox false
> show scale bar
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> scalebar bar
Expected a number or a keyword
> scalebar bar 100
Expected a number or a keyword
> scalebar 100
> save /Users/Mocki004/Desktop/image9.png supersample 3
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_sideView.png
> width 3840 height 2342 supersample 2 transparentBackground true
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice.cxs
> ui tool show "Surface Color"
> color radial #1.1.1 palette #ff0000:#ffffff:#0000ff
> color single #1.1.1
> ui tool show "Color Zone"
> show #!3 models
> volume #3 level 0.06265
> color #1 #ffffff0a models
> color #1 #ffffff00 models
> show #!5 models
Window position QRect(1985,863 575x242) outside any known screen, using
primary screen
Window position QRect(1985,358 575x671) outside any known screen, using
primary screen
> volume #1 level 0.05223
> view orient
> view
[Repeated 1 time(s)]
> volume #1 region 26,0,0,129,120,57
> volume #1 region 26,0,0,95,120,57
> volume #1 region 26,0,10,95,120,57
> volume #1 region 26,0,10,95,97,57
> volume #3 region 0,0,8,129,120,23
> hide #!3 models
> hide #!5 models
> hide #!7 models
> volume #1 region 26,8,10,95,97,57
> volume #1 region 26,8,10,95,97,49
> show #!3 models
> show #!5 models
> volume #1 region 26,8,10,95,101,49
> volume #3 region 0,0,8,129,98,23
> volume #3 region 24,0,8,129,98,23
> volume #3 region 24,10,8,129,98,23
> volume #3 region 24,10,8,97,98,23
> volume #5 region 0,0,0,76,83,15
> color #1 #ffffff21 models
> color #1 #ffffff11 models
> color #1 #ffffff1a models
> volume #5 region 0,0,0,76,83,15
> volume #1 region 26,13,10,95,101,49
> volume #1 region 26,16,10,95,101,49
> volume #1 region 26,16,10,95,97,49
> volume #1 region 26,16,10,99,97,49
> volume #3 region 24,10,8,99,98,23
> volume #3 region 24,10,8,100,98,23
> volume #5 region 0,0,0,76,83,15
> volume #1 region 26,18,10,99,97,49
> volume #3 region 24,15,8,100,98,23
> lighting shadows true intensity 0.5
Drag select of 1 251124_postprocess_cropped.mrc , 3
251124_postprocess_cropped_INM.mrc , 5 251124_postprocess_cropped_ONM.mrc
> volume #1 region 26,18,10,99,62,49
> volume #1 region 26,18,10,99,67,49
> volume #1 region 26,33,10,99,67,49
[Repeated 1 time(s)]
> volume #1 region 26,42,10,99,67,49
> volume #1 region 26,56,10,99,68,49
> volume #1 region 26,56,10,99,65,49
> volume #5 region 0,43,0,76,83,15
> volume #5 region 0,40,0,76,83,15
> volume #3 region 24,62,8,100,98,23
> volume #1 region 26,59,10,99,65,49
> volume #3 region 24,58,8,100,98,23
> volume #1 region 26,57,10,99,65,49
> volume #5 region 0,40,0,76,49,15
> volume #3 region 24,58,8,100,61,23
> select clear
> volume #1 region 26,57,10,99,61,49
> volume #1 region 26,47,10,99,61,49
> volume #1 region 26,47,10,99,64,49
> volume #1 region 26,47,10,99,66,49
> volume #1 region 26,59,10,99,66,49
> volume #1 region 26,59,10,99,64,49
[Repeated 1 time(s)]
> volume #5 region 0,48,0,76,49,15
> volume #3 region 24,59,8,100,61,23
> volume #3 region 24,59,8,100,65,23
> volume #3 region 24,64,8,100,65,23
> volume #1 region 26,65,10,99,65,49
> volume #1 region 26,65,10,99,71,49
> volume #1 region 26,57,10,99,60,49
> volume #1 level 0.03902
> volume #1 level 0.03737
> volume #5 region 0,42,0,76,43,15
> volume #3 region 24,36,8,100,64,23
> volume #3 region 24,57,8,100,64,23
> volume #3 region 24,57,8,100,60,23
> volume #1 region 26,57,10,99,59,49
> volume #1 region 26,59,10,99,59,49
> volume #6 level 0.02912
> volume #5 region 0,0,0,76,43,15
> volume #5 region 0,0,0,76,83,15
> volume #1 region 26,59,10,99,120,49
> volume #1 region 26,0,10,99,120,49
> volume #1 region 26,0,10,99,120,57
> volume #1 region 26,0,10,65,120,57
> volume #3 region 24,0,8,100,60,23
> volume #3 region 24,0,8,100,120,23
> volume #5 region 0,0,0,76,83,15
> volume #1 region 26,0,10,65,120,57
> volume #1 region 26,0,10,129,120,57
> hide #!1 models
> volume #3 region 24,0,8,129,120,23
> volume #5 region 0,0,0,77,83,15
[Repeated 3 time(s)]
> hide #!5 models
> show #!5 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.08793
> volume #5 level 0.07405
> show #!1 models
> hide #!5 models
> hide #!6 models
> volume #1 region 26,0,10,129,120,41
> volume #1 region 26,0,16,129,120,41
> volume #1 region 26,0,16,129,117,41
> volume #1 region 26,0,16,129,66,41
> volume #1 region 26,0,16,129,78,41
[Repeated 1 time(s)]
> volume #1 region 26,0,16,129,78,40
> volume #1 region 26,0,16,129,78,41
[Repeated 2 time(s)]
> volume #!1 showOutlineBox true
> volume #1 region 26,0,16,129,99,41
> show #!5 models
> show #!3 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!1 models
> hide #!3 models
> volume #!5 showOutlineBox true
> volume #5 region 0,0,0,77,83,15
[Repeated 3 time(s)]
> volume #5 region 0,0,0,77,83,14
> show #!1 models
> hide #!1 models
> volume #5 region 0,0,0,77,83,15
> show #!1 models
> show #!3 models
> volume #1 level 0.05768
> volume #!1,3,5 showOutlineBox false
> view orient
> turn x -90
> ui tool show "Side View"
> lighting soft
> lighting flat
> hide #!5 models
> hide #!3 models
> volume #1 region 26,0,16,129,99,57
> volume #1 region 26,0,0,129,99,57
> view
> lighting flat
> ui tool show "Segment Map"
> volume #1 region 26,0,0,80,99,57
> volume #1 region 26,0,0,61,99,57
> volume #1 region 26,0,0,92,99,57
> view orient
> turn x -90
> ui tool show "Side View"
> view orient
> view
> volume #1 region 26,0,0,129,99,57
> volume #1 region 0,0,0,129,99,57
> volume #1 region 0,0,0,129,120,57
> ui tool show "Side View"
> lighting flat
> volume #1 region 0,0,0,129,65,57
> volume #1 region 0,0,0,129,120,57
> ui mousemode right clip
> ui mousemode right "clip rotate"
> view orient
> view
> turn x -90
> turn y30
Expected an axis vector or a keyword
> turn y30
Expected an axis vector or a keyword
> turn y 30
> ui mousemode right clip
Drag select of 1 251124_postprocess_cropped.mrc
> select clear
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "crop volume"
> volume #1 region 0,44,0,129,120,57
> volume #1 region 0,44,0,129,84,57
> volume #1 region 0,44,0,99,84,57
> volume #1 region 18,44,0,99,84,57
> volume #1 region 18,42,0,99,84,57
> volume #1 region 18,42,0,103,84,57
[Repeated 1 time(s)]
> volume #1 region 18,41,0,103,48,57
> volume #1 region 18,42,0,103,48,57
> volume #1 region 18,42,0,103,45,57
> volume #1 region 18,0,0,103,45,57
> volume #1 region 18,0,0,103,120,57
> volume #1 region 18,0,0,129,120,57
> volume #1 region 74,0,0,129,120,57
> volume #1 region 0,0,0,129,120,57
> volume #1 region 0,0,0,129,92,57
> volume #1 region 0,0,0,129,85,57
> volume #1 level 0.04113
> volume #1 level 0.05332
> volume #1 region 0,0,0,129,70,57
> volume #1 region 0,68,0,129,70,57
> volume #1 region 0,68,0,129,75,57
> volume #1 region 0,68,0,129,78,57
> color #6 #ffffff00 models
> color #2.2 #00000072
> color #2.1 #9e9e9e72
> color #2.1 #9e9e9eff
> color #2.3 #318d67ff
> color #2.1 #7faa99ff
> color #2.2 transparent
> graphics silhouettes false
> graphics silhouettes true
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice.cxs
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice_v2.cxs
——— End of log from Mon Nov 24 17:14:09 2025 ———
opened ChimeraX session
Showing 251124_postprocess_cropped.seg - 3 regions, 3 surfaces
> hide #2.3 models
> hide #2.2 models
> hide #2.1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #2.1 models
> show #2.3 models
> hide #2.1 models
> select #2.3
1 model selected
Ungrouped to 2 regions
> select #2.4
1 model selected
Ungrouped to 2 regions
Ungrouped to 6 regions
[Repeated 1 time(s)]Ungrouped to 8 regions
Ungrouped to 29 regions
Ungrouped to 12 regions
Ungrouped to 4 regions
Ungrouped to 11 regions
Ungrouped to 21 regions
Ungrouped to 34 regions
Ungrouped to 12 regions
Ungrouped to 3 regions
Ungrouped to 2 regions
Ungrouped to 9 regions
Ungrouped to 19 regions
Ungrouped to 9 regions
> select #2.145
1 model selected
> select add #2.127
2 models selected
> select add #2.14
3 models selected
> select add #2.74
4 models selected
Grouped 4 regions
> select #2.146
1 model selected
Ungrouped to 2 regions
> select #2.74
1 model selected
> select add #2.14
2 models selected
Grouped 2 regions
> select #2.5
1 model selected
> select add #2.138
2 models selected
> select #2.14
1 model selected
> select add #2.138
2 models selected
> select add #2.135
3 models selected
Grouped 3 regions
> select #2.136
1 model selected
Ungrouped to 0 regions
> select #2.120
1 model selected
> select add #2.126
2 models selected
> select subtract #2.126
1 model selected
> select add #2.122
2 models selected
Drag select of 4443, 529 of 56456 triangles
> select clear
> select #2.120
1 model selected
> select add #2.14
2 models selected
> select add #2.71
3 models selected
Grouped 3 regions
> select #2.4
1 model selected
> select clear
> select #2.14
1 model selected
> select #2.14
1 model selected
> select add #2.5
2 models selected
Grouped 2 regions
> select #2.1
1 model selected
> select clear
Drag select of 4439, 213001 of 213220 triangles, 1949, 1951, 2238, 2516, 1952,
1947, 1948, 2171, 1820, 2024, 1796, 1742, 3478, 2792, 1913, 1909, 1908, 1811,
2019, 1906, 2446, 2027, 2039, 1812, 1915, 1916, 1919, 2466, 2178, 2629, 3135,
1910, 1912, 2796, 2175, 2319, 1804, 2027 of 2048 triangles, 3068, 1902, 2700,
1845, 1793, 1342 of 1356 triangles, 1794, 2244 of 2408 triangles, 2150, 1922,
2185, 1850, 1942, 2369, 1939, 1941, 2603, 1846, 1943, 1930, 1880, 1768, 1740,
1934, 2051, 1836, 2046, 2047, 2048, 2333, 1827, 1892, 1895, 1889, 2013, 1783,
1771, 2418, 2106, 2112, 1788, 2297, 1773, 3451, 2006, 1772, 1893, 2284, 2754,
2012, 2117, 2011, 3463, 2944, 2292, 2110, 2766, 2770, 1797, 1896, 2129, 2153,
2008, 2118, 1991, 2691, 1888, 2282, 2287, 2753, 2760, 1757, 1853, 1832, 1929,
1829, 1931, 1928, 2044, 1926, 1762, 1731, 2744 of 2788 triangles, 1873, 1885,
1936, 2339, 1736, 3285 of 3316 triangles, 1839, 1842, 1822, 1925, 2403, 1894,
2104, 4419, 1763, 2155
Grouped 133 regions
> color #2 white
> select clear
> undo
[Repeated 1 time(s)]
> select clear
> show #2.1 models
> show #2.5 models
> hide #2.5 models
> show #2.5 models
> hide #2.5 models
> hide #2.2 models
> show #2.2 models
> color #3 #8c8c8cff models
> show #!4 models
> hide #2.2 models
> hide #2.1 models
> color #4 #b0b0b0ff models
> color #4 #a0a0a0ff models
> color #4 #318d67ff models
> color #4 #7faa99ff models
> hide #!4 models
> set bgColor gray
> show #2.5 models
> hide #2.5 models
> show #2.2 models
> show #2.5 models
> hide #2.5 models
> show #2.5 models
> hide #2.5 models
> hide #2.2 models
> color #2.1 #7faa99ff
> color #2.2 #318d67ff
> hide #!2 models
> show #!1 models
> set bgColor white
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice_v2.cxs
> ui mousemode right "crop volume"
> volume #1 region 0,14,0,129,78,57
> volume #1 region 0,14,0,129,120,57
> volume #1 region 0,14,0,129,120,32
> volume #1 region 0,0,0,129,120,32
> show #!7 models
> ui mousemode right translate
> volume #1 level 0.06987
> ui tool show "Side View"
> view orient
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_chimX_snaps/251124_onm_v1.png
> width 3640 height 2220 supersample 2 transparentBackground true
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting flat
> lighting soft
> ui mousemode right "crop volume"
> volume #1 region 0,0,0,129,64,32
> volume #1 region 0,39,0,129,64,32
> volume #1 region 0,39,0,129,109,32
> volume #1 region 0,29,0,129,109,32
> volume #1 level 0.06116
> volume #1 region 0,29,0,129,64,32
> volume #1 region 0,29,0,129,68,32
> volume #1 region 0,43,0,129,77,32
> volume #1 region 0,43,0,129,77,57
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice_v3.cxs
> volume #1 region 0,43,0,129,69,57
> volume #1 level 0.04984
> view orient
> turn x -90
> turn y 180
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_chimX_snaps/251124_sideView_v4_soft_w-
> shadow.png width 3840 height 2342 supersample 2 transparentBackground true
> volume #1 region 0,35,0,129,120,57
[Repeated 1 time(s)]
> volume #1 region 0,0,0,129,120,57
> volume #1 region 0,0,0,129,120,35
> color #2.5 #fafafaff
> color #2.5 #f7f7f7ff
> color #2.5 white
> view orient
> turn y180
Expected an axis vector or a keyword
> turn y 180
[Repeated 1 time(s)]
> turn x -90
> turn y180
Expected an axis vector or a keyword
> turn y 180
> turn x 90
> ui mousemode right translate
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_chimX_snaps/251124_onm_v2_soft_w-
> shadow.png width 3840 height 2342 supersample 2 transparentBackground true
> ui mousemode right "crop volume"
> volume #1 region 0,0,0,129,120,57
> volume #1 region 0,0,40,129,120,57
> volume #1 region 0,0,34,129,120,57
> volume #1 level 0.03048
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_v3.seg
> models #2
> open /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_v3_for_inm.seg
Summary of feedback from opening
/Users/Mocki004/Library/CloudStorage/OneDrive-
UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_v3_for_inm.seg
---
note | Showing 3 region surfaces
Opened 251124_postprocess_cropped_v3_for_inm.seg
> hide #!1 models
> hide #8.2 models
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1 model selected
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1 model selected
Ungrouped to 754 regions
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3 models selected
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4 models selected
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5 models selected
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Grouped 11 regions
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2 models selected
Grouped 2 regions
> color #8.1 #c9c9c9ff
> color #8.1 white
> select clear
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> color #2.2 #8c8c8cff
> color #2.2 #797979ff
> color #8.3 #797979ff
> color #8.3 #318d67ff
> hide #8.3 models
> show #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Showing 251124_postprocess_cropped_v3_for_inm.seg - 4 regions, 4 surfaces
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Map 251124_postprocess_cropped.mrc is now associated with
251124_postprocess_cropped_v3_for_inm.seg
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_postprocess_cropped_v3_for_inm.seg
> models #8
> save /Users/Mocki004/Library/CloudStorage/OneDrive-
> UniversiteitUtrecht/UU/Publication/002_LINC_complexes/PNAS_revision/figures/5_averaging/human_lattice/PostProcess_job345/251124_segmentation_lattice_v3.cxs
——— End of log from Mon Nov 24 18:03:54 2025 ———
> view name session-start
opened ChimeraX session
> hide #!7 models
> hide #!8 models
> hide #8.1 models
> hide #8.2 models
> hide #8.3 models
> hide #8.4 models
> hide #!1 models
> show #!1 models
> ui mousemode right "crop volume"
> volume #1 region 0,0,0,129,120,57
> volume #1 region 0,0,0,129,84,57
> volume #1 region 0,19,0,129,84,57
> volume #1 region 0,19,0,129,99,57
> volume #1 region 38,19,0,129,99,57
> volume #1 region 38,19,0,115,99,57
> volume #1 region 38,19,0,115,99,33
> volume #1 region 0,19,0,115,99,33
> volume #1 region 0,0,0,115,99,33
> volume #1 region 0,0,0,129,99,33
> volume #1 region 0,0,0,129,120,33
> color #8.1 #f5974fff
> color #8.1 #f5c34fff
> volume #1 region 0,0,0,129,120,57
> volume #1 region 0,0,23,129,120,57
> volume #1 region 0,0,34,129,120,57
> color #8.3 #f5c34fff
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15W003U8N/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.41.1
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.2 (24G325)
Kernel Version: Darwin 24.6.0
Time since boot: 20 days, 16 hours, 54 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
HP E273q:
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UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
geomdl: 5.4.0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
pandas: 2.3.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pyarrow: 21.0.0
pycollada: 0.8
pydantic: 2.11.7
pydantic_core: 2.33.2
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
starfile: 0.5.13
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing-inspection: 0.4.1
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 6 days ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 6 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel said what we know about this crash:
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
We have not observed this crash in the ChimeraX 1.11 release candidate or daily build which use a newer Qt version, so you might want to try those.
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Reported by Jonas Moecking