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Opened 3 months ago
Closed 3 months ago
#18316 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-15.4.1-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.
Fatal Python error: Bus error
Current thread 0x00000001f62b0c80 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imaging, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio (total: 48)
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===== Log before crash start =====
UCSF 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/annguyen/Downloads/cryosparc_P12_J230_001_volume_map (1).mrc"
Opened cryosparc_P12_J230_001_volume_map (1).mrc as #1, grid size 100,100,100,
pixel 5.73, shown at level 1.38, step 1, values float32
> open "/Users/annguyen/Downloads/cryosparc_P12_J279_001_volume_map (1).mrc"
Opened cryosparc_P12_J279_001_volume_map (1).mrc as #2, grid size 100,100,100,
pixel 5.73, shown at level 1.1, step 1, values float32
> volume #1 level 0.1117
> open 7old fromDatabase pdb format mmcif
7old title:
Thermophilic eukaryotic 80S ribosome at pe/E (TI)-POST state [more info...]
Chain information for 7old #3
---
Chain | Description | UniProt
1 | 26S rRNA |
2 | 18S rRNA |
3 | 5S rRNA |
4 | 5.8S rRNA |
5 | pe/E tRNA |
A | Putative guanine nucleotide-binding protein | G0S9U0_CHATD 1-316
B | HABP4_PAI-RBP1 domain-containing protein | G0S428_CHATD 1-302
C | Elongation factor 2 | G0S5T7_CHATD 1-845
LA | 60S ribosomal protein L2-like protein | G0S4P8_CHATD 1-254
LB | 60S ribosomal protein L3-like protein | G0RXW1_CHATD 1-392
LC | 60S ribosomal protein L4-like protein | G0SFC3_CHATD 1-365
LD | 60S ribosomal protein l5-like protein | G0SEG2_CHATD 1-304
LE | 60S ribosomal protein L6 | G0S0D6_CHATD 1-200
LF | 60S ribosomal protein l7-like protein | G0SFL0_CHATD 1-249
LG | 60S ribosomal protein L8 | G0SAJ9_CHATD 1-262
LH | 60S ribosomal protein l9-like protein | G0S0E5_CHATD 1-229
LI | 60S ribosomal protein L10-like protein | G0SEI1_CHATD 1-219
LJ | Putative ribosomal protein | G0SHQ2_CHATD 1-173
LK | 60S ribosomal protein L12-like protein | G0SGH8_CHATD 1-165
LL | 60S ribosomal protein L13 | G0S992_CHATD 1-213
LM | 60S ribosomal protein L14-like protein | G0S1R0_CHATD 1-142
LN | Ribosomal protein L15 | G0RZ88_CHATD 1-203
LO | 60S ribosomal protein L16-like protein | G0SH61_CHATD 1-204
LP | 60S ribosomal protein l17-like protein | G0SGY1_CHATD 1-187
LQ | Ribosomal protein L18-like protein | G0S9B5_CHATD 1-213
LR | Ribosomal protein L19 | G0S9T3_CHATD 1-192
LS | 60S ribosomal protein L20 | G0SCE2_CHATD 1-174
LT | 60S ribosomal protein l21-like protein | G0S0Z3_CHATD 1-160
LU | 60S ribosomal protein L22-like protein | G0SDS8_CHATD 1-127
LV | 60S ribosomal protein l23-like protein | G0SI44_CHATD 1-139
LW | 60S ribosomal protein L24-like protein | G0S1P9_CHATD 1-205
LX | 60S ribosomal protein L25-like protein | G0S507_CHATD 1-156
LY | 60S ribosomal protein L26-like protein | G0RYN9_CHATD 1-138
LZ | 60S ribosomal protein L27 | G0RZE9_CHATD 1-135
La | 60S ribosomal protein L28-like protein |
Lb | 60S ribosomal protein L29 | Q2H9W4_CHAGB 1-65
Lc | 60S ribosomal protein l30-like protein | G0SEI0_CHATD 1-108
Ld | Putative 60S ribosomal protein | G0SD68_CHATD 4-123
Le | 60S ribosomal protein L32-like protein | G0S6V4_CHATD 1-131
Lf | 60S ribosomal protein l33-like protein | G0SCL3_CHATD 1-109
Lg | Ribosomal protein l34-like protein | G0SFN0_CHATD 1-119
Lh | Dolichyl-diphosphooligosaccharide--protein glycotransferase | G0S0D7_CHATD 1-126
Li | 60S ribosomal protein L36 | G0SBN1_CHATD 1-110
Lj | Ribosomal protein L37 | G0S101_CHATD 1-95
Lk | 60S ribosomal protein L38-like protein | G0SG89_CHATD 1-81
Ll | Ribosomal protein eL39 | Q2H9R2_CHAGB 1-51
Lm | Ubiquitin | G0S8G4_CHATD 3-128
Ln Lr | 60S ribosomal protein L41-A | RL41A_YEAST 1-25
Lo | 60S ribosomal protein L44-like protein | G0SBZ6_CHATD 1-106
Lp | 60S ribosomal protein L43-like protein | G0S6B0_CHATD 1-92
Lq | Putative 60S ribosomal protein | G0SHJ6_CHATD 1-147
Ls | 60S acidic ribosomal protein P0 | G0SGP3_CHATD 1-312
SA | 40S ribosomal protein S0 | G0RYF9_CHATD 1-285
SB | 40S ribosomal protein S1 | G0S7T8_CHATD 1-255
SC | 40S ribosomal protein S2-like protein | G0SAV4_CHATD 1-263
SD | 40S ribosomal protein S3-like protein | G0S6I7_CHATD 1-254
SE | 40S ribosomal protein S4 | G0S1A6_CHATD 1-264
SF | 40S ribosomal protein s5-like protein | G0S1Z0_CHATD 1-212
SG | 40S ribosomal protein S6 | G0RY43_CHATD 1-239
SH | 40S ribosomal protein S7 | G0S8C4_CHATD 1-203
SI | 40S ribosomal protein S8 | G0RY45_CHATD 1-202
SJ | 40S ribosomal protein s9-like protein | G0S0Z4_CHATD 1-190
SK | 40S ribosomal protein s10-like protein | G0RZD8_CHATD 1-159
SL | 40S ribosomal protein S11-like protein | G0SF00_CHATD 1-161
SM | 40S ribosomal protein S12 | G0SHH9_CHATD 1-144
SN | 40S ribosomal protein S13-like protein | G0RZM9_CHATD 1-151
SO | 40S ribosomal protein S14-like protein | G0SFL1_CHATD 1-150
SP | 40S ribosomal protein s15-like protein | G0S084_CHATD 1-153
SQ | 40S ribosomal protein S16-like protein | G0SBR7_CHATD 1-143
SR | 40S ribosomal protein S17-like protein | G0S871_CHATD 1-143
SS | Putative ribosomal protein | G0S6J7_CHATD 1-156
ST | 40S ribosomal protein S19-like protein | G0SFK8_CHATD 1-153
SU | 40S ribosomal protein S20-like protein | G0S379_CHATD 1-116
SV | 40S ribosomal protein S21-like protein | G0SI21_CHATD 1-98
SW | 40S ribosomal protein S22-like protein | G0SHI0_CHATD 1-130
SX | 40S ribosomal protein s23-like protein | G0RY17_CHATD 1-145
SY | 40S ribosomal protein S24 | RS24_CHATD 1-136
SZ | 40S ribosomal protein S25 | G0S1Y9_CHATD 1-99
Sa | 40S ribosomal protein S26 | G0S2X4_CHATD 1-119
Sb | Ribosomal protein s27-like protein | G0S1S4_CHATD 1-82
Sc | 40S ribosomal protein S28-like protein | G0S9M9_CHATD 1-68
Sd | Ribosomal protein uS14 | Q2HB68_CHAGB 1-56
Se | 40S ribosomal protein S30 | Q2H4C5_CHAGB 1-62
Sf | 40S ribosomal protein S27a-like protein | G0S2X5_CHATD 1-154
Non-standard residues in 7old #3
---
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
GDP — guanosine-5'-diphosphate
MG — magnesium ion
ZN — zinc ion
> hide atoms
> show cartoons
Enter a PDB ID in the entry field
Mismatch between Cocoa 'v' and Carbon '\x0' for virtual key 9 with
QFlags(NoModifier)
Mismatch between Cocoa 'V' and Carbon '\x0' for virtual key 9 with
QFlags(ShiftModifier)
Mismatch between Cocoa 'v' and Carbon '\x0' for virtual key 9 with
QFlags(ControlModifier)
Mismatch between Cocoa 'v' and Carbon '\x0' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\u221a' and Carbon '\x0' for virtual key 9 with
QFlags(AltModifier)
Mismatch between Cocoa '\u25ca' and Carbon '\x0' for virtual key 9 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\u221a' and Carbon '\x0' for virtual key 9 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\u25ca' and Carbon '\x0' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open 8bf9 fromDatabase pdb format mmcif
Summary of feedback from opening 8bf9 fetched from pdb
---
note | Fetching compressed mmCIF 8bf9 from http://files.rcsb.org/download/8bf9.cif
8bf9 title:
Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. [more
info...]
Chain information for 8bf9 #4
---
Chain | Description | UniProt
5 | RNA (1766) |
8 | RNA (156-MER) |
A | Translocon-associated protein subunit alpha |
B | Translocon-associated protein subunit beta | W5P572_SHEEP 1-186
C | Sec61a |
D | Translocon-associated protein subunit delta | W5P940_SHEEP 1-173
G | Translocon-associated protein subunit gamma | W5NYA9_SHEEP 1-185
P | Large ribosomal subunit protein uL22 | W5Q9T9_SHEEP 1-184
R | Ribosomal protein L19 | W5PLN0_SHEEP 1-196
U | RL22 protein (Fragment) | A0A6P7EJM7_SHEEP 1-128
X | Ribosomal protein L23/L25 N-terminal domain-containing protein | A0A6P3CX48_SHEEP 1-156
Y | RL26 protein (Fragment) | A0A7K9BN74_9PICI 1-134
b | Sec61b |
d | Large ribosomal subunit protein eL31 | W5PUU0_SHEEP 1-125
g | Protein transport protein Sec61 subunit gamma | A0A836CVU8_SHEEP -5-75
h | Large ribosomal subunit protein uL29 | A0A6P3TAC5_SHEEP 1-123
j | Ribosomal protein L37 | W5P472_SHEEP 1-97
k | Large ribosomal subunit protein eL38 |
l | 60S ribosomal protein L39 |
> show cartoons
> hide atoms
> ui mousemode right "translate selected models"
> select add #4
55482 atoms, 60473 bonds, 1730 pseudobonds, 3914 residues, 3 models selected
> view matrix models #4,1,0,0,-430.48,0,1,0,148.55,0,0,1,-122.58
> select subtract #4
Nothing selected
> select add #3
214209 atoms, 229425 bonds, 4810 pseudobonds, 17997 residues, 4 models
selected
> view matrix models #3,1,0,0,129.21,0,1,0,-201.06,0,0,1,-11.791
> view matrix models #3,1,0,0,-108.26,0,1,0,-180.88,0,0,1,-268.29
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.14613,-0.15801,0.97656,-97.466,-0.85875,-0.51032,0.045932,418.99,0.49111,-0.84534,-0.21027,133.56
> view matrix models
> #3,0.28427,-0.25084,0.92535,-100.18,-0.87968,-0.45205,0.1477,382.48,0.38125,-0.856,-0.34917,206.26
> ui mousemode right "move picked models"
> view matrix models
> #3,0.28427,-0.25084,0.92535,-153.65,-0.87968,-0.45205,0.1477,505.59,0.38125,-0.856,-0.34917,500.54
> view matrix models
> #3,0.28427,-0.25084,0.92535,-56.372,-0.87968,-0.45205,0.1477,606.9,0.38125,-0.856,-0.34917,594.17
> view matrix models
> #3,0.28427,-0.25084,0.92535,-12.885,-0.87968,-0.45205,0.1477,596.31,0.38125,-0.856,-0.34917,498.5
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule 7old (#3) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1)
using 214209 atoms
average map value = 0.7378, steps = 196
shifted from previous position = 32.4
rotated from previous position = 36.9 degrees
atoms outside contour = 55126, contour level = 0.11166
Position of 7old (#3) relative to cryosparc_P12_J230_001_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
0.47481197 0.34239392 0.81075273 -156.74890563
-0.67940501 -0.44297390 0.58496405 421.78272722
0.55943044 -0.82857741 0.02229483 347.78131290
Axis -0.80214761 0.14261879 -0.57984402
Axis point 0.00000000 323.22435899 72.43629804
Rotation angle (degrees) 118.22488875
Shift along axis -15.76901128
> color #1 #b2b2b2b7 models
> view matrix models #1,1,0,0,-222.47,0,1,0,-46.584,0,0,1,-150.86
> view matrix models
> #3,0.47481,0.34239,0.81075,-166.98,-0.67941,-0.44297,0.58496,433.9,0.55943,-0.82858,0.022295,352.6
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.47503,-0.030968,-0.87943,666.16,0.38634,0.89057,-0.24004,34.685,0.79063,-0.45379,-0.41108,316.06
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.47503,-0.030968,-0.87943,616.34,0.38634,0.89057,-0.24004,99.968,0.79063,-0.45379,-0.41108,177.74
> view matrix models
> #3,-0.47503,-0.030968,-0.87943,427.62,0.38634,0.89057,-0.24004,-4.4885,0.79063,-0.45379,-0.41108,211.25
> fitmap #3 inMap #1
Fit molecule 7old (#3) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1)
using 214209 atoms
average map value = 1.244, steps = 96
shifted from previous position = 67.4
rotated from previous position = 15.6 degrees
atoms outside contour = 2514, contour level = 0.11166
Position of 7old (#3) relative to cryosparc_P12_J230_001_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
-0.61311858 -0.19110802 -0.76652680 707.61475725
0.35557936 0.79969249 -0.48379256 107.85702207
0.70544235 -0.56918332 -0.42235226 359.80518554
Axis -0.05430150 -0.93605132 0.34764821
Axis point 255.98611489 0.00000000 383.42085790
Rotation angle (degrees) 128.16215440
Shift along axis -14.29862127
> view matrix models
> #3,-0.61312,-0.19111,-0.76653,515.58,0.35558,0.79969,-0.48379,58.407,0.70544,-0.56918,-0.42235,192.28
> undo
> select subtract #3
Nothing selected
> select add #3
214209 atoms, 229425 bonds, 4810 pseudobonds, 17997 residues, 4 models
selected
> select subtract #3
Nothing selected
> select add #4
55482 atoms, 60473 bonds, 1730 pseudobonds, 3914 residues, 3 models selected
> view matrix models #4,1,0,0,-330.9,0,1,0,125.38,0,0,1,-170.27
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.63642,0.68218,-0.35999,43.252,0.69404,0.71009,0.11864,-20.981,0.33656,-0.17434,-0.92538,476.53
> view matrix models
> #4,0.65578,0.02597,-0.75451,35.734,0.57232,0.63467,0.51928,-94.691,0.49234,-0.77235,0.40134,194.25
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.65578,0.02597,-0.75451,1.5827,0.57232,0.63467,0.51928,-312.88,0.49234,-0.77235,0.40134,108.54
> view matrix models
> #4,0.65578,0.02597,-0.75451,117.69,0.57232,0.63467,0.51928,-295.2,0.49234,-0.77235,0.40134,94.404
> view matrix models
> #4,0.65578,0.02597,-0.75451,131.59,0.57232,0.63467,0.51928,-319.36,0.49234,-0.77235,0.40134,74.668
> fitmap #4 inMap #1
Fit molecule 8bf9 (#4) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1)
using 55482 atoms
average map value = 1.003, steps = 160
shifted from previous position = 33.6
rotated from previous position = 27.7 degrees
atoms outside contour = 7113, contour level = 0.11166
Position of 8bf9 (#4) relative to cryosparc_P12_J230_001_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
0.61337148 0.21051822 -0.76122106 293.92775943
0.20676955 0.88740241 0.41202344 -240.94324241
0.76224785 -0.41012077 0.50077857 -15.43390777
Axis -0.47491119 -0.88003106 -0.00216541
Axis point 227.02612225 0.00000000 316.03855197
Rotation angle (degrees) 59.94863156
Shift along axis 72.48137520
> undo
> toolshed show
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.98305,0.16823,-0.072841,337.76,0.16816,0.98573,0.0071961,-125.24,0.073012,-0.0051744,-0.99732,418.27
> view matrix models
> #4,-0.791,-0.29959,0.53344,248.01,-0.33169,0.94264,0.037568,39.409,-0.5141,-0.14722,-0.845,606.66
> view matrix models
> #4,-0.93733,0.015697,0.3481,234.54,-0.024501,0.99354,-0.11078,-25.446,-0.34759,-0.11236,-0.93089,570.55
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.93733,0.015697,0.3481,207.6,-0.024501,0.99354,-0.11078,-28.23,-0.34759,-0.11236,-0.93089,606.33
> view matrix models
> #4,-0.93733,0.015697,0.3481,211.07,-0.024501,0.99354,-0.11078,-20.698,-0.34759,-0.11236,-0.93089,612.89
> fitmap #4 inMap #1
Fit molecule 8bf9 (#4) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1)
using 55482 atoms
average map value = 1.274, steps = 104
shifted from previous position = 40.8
rotated from previous position = 23.5 degrees
atoms outside contour = 5888, contour level = 0.11166
Position of 8bf9 (#4) relative to cryosparc_P12_J230_001_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
-0.99984326 0.01309177 0.01191864 607.92104186
0.01430173 0.99406427 0.10785026 -80.76132776
-0.01043594 0.10800381 -0.99409570 576.19775515
Axis 0.00685881 0.99851492 0.05404546
Axis point 305.85968810 0.00000000 288.57980617
Rotation angle (degrees) 179.35862267
Shift along axis -45.33090597
> volume #1 level 0.1577
Enter a PDB ID in the entry field
> open 3j7r fromDatabase pdb format mmcif
Summary of feedback from opening 3j7r fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue template for U /S4:15
Atom OP2 has no neighbors to form bonds with according to residue template for
U /S4:15
3j7r title:
Structure of the translating mammalian ribosome-Sec61 complex [more info...]
Chain information for 3j7r #5
---
Chain | Description | UniProt
1 | Sec61 alpha subunit | A0A4X1TV07_PIG 25-466
2 | Sec61 gamma subunit | A0A480WFL1_PIG 1-68
3 | Sec61 beta subunit |
5 | 28S ribosomal RNA |
7 | 5S ribosomal RNA |
8 | 5.8S ribosomal RNA |
A | Ribosomal protein uL2 | A0A480Q387_PIG 1-257
B | Ribosomal protein uL3 | A0A480L253_PIG 2-395
C | Ribosomal protein uL4 | A0A287AE76_PIG 2-368
D | Ribosomal protein uL18 | A0A287ASD0_PIG 1-297
E | Ribosomal protein eL6 | RL6_PIG 38-284
F | Ribosomal protein uL30 | A0A480W0U3_PIG 26-250
G | Ribosomal protein eL8 | A0A4X1W808_PIG 1-266
H | Ribosomal protein uL6 | I3LP78_PIG 1-192
I | Ribosomal protein uL16 | RL10_PIG 2-214
J | Ribosomal protein uL5 | RL11_PIG 1-178
L | Ribosomal protein eL13 | A0A4X1TBV3_PIG 1-211
M | Ribosomal protein eL14 | RL14_PIG 1-213
N | Ribosomal protein eL15 | A0A286ZL65_PIG 1-204
O | Ribosomal protein uL13 | A0A480L469_PIG 3-203
P | Ribosomal protein uL22 | A0A287B386_PIG 2-154
Q | Ribosomal protein eL18 | A0A4X1W0N5_PIG 1-188
R | Ribosomal protein eL19 | A0A480VXS3_PIG 2-196
S | Ribosomal protein eL20 | A0A287APR1_PIG -47-176
S2 | 18S ribosomal RNA |
S4 | Messenger RNA |
S5 | A/P tRNA |
S6 | P/E tRNA |
SA | Ribosomal protein uS2 | RSSA_PIG 1-295
SB | Ribosomal protein eS1 | B6V8C8_PIG 1-264
SC | Ribosomal protein uS5 | I3LJ87_PIG 59-276
SD | Ribosomal protein uS3 | RS3_PIG 1-243
SE | Ribosomal protein eS4 | A0A4X1W0I3_PIG 1-263
SF | Ribosomal protein uS7 | F2Z5E6_PIG 1-204
SG | Ribosomal protein eS6 | A0A480E3J4_PIG 1-249
SH | Ribosomal protein eS7 | A0A287A9Y6_PIG 1-194
SI | Ribosomal protein eS8 | A0A480YST6_PIG 1-208
SJ | Ribosomal protein uS4 | A0A480Q6G1_PIG 1-194
SK | Ribosomal protein eS10 | A0A480EHW2_PIG 1-165
SL | Ribosomal protein uS17 | A0A480QMH2_PIG 1-158
SM | Ribosomal protein eS12 | RS12_PIG 9-132
SN | Ribosomal protein uS15 | F6Q5P0_PIG 1-151
SO | Ribosomal protein uS11 |
SP | Ribosomal protein uS19 | RS15_PIG 1-145
SQ | Ribosomal protein uS9 | RS16_PIG 1-146
SR | Ribosomal protein eS17 | RS17_PIG 1-135
SS | Ribosomal protein uS13 | RS18_PIG 1-152
ST | Ribosomal protein eS19 | A0A4X1SDD8_PIG 1-145
SU | Ribosomal protein uS10 | RS20_PIG 1-119
SV | Ribosomal protein eS21 | RS21_PIG 1-83
SW | Ribosomal protein uS8 | A0A480KS86_PIG 1-130
SX | Ribosomal protein uS12 | RS23_PIG 1-143
SY | Ribosomal protein eS24 | A0A4X1SJK8_PIG 1-132
SZ | Ribosomal protein es25 | A0A480V055_PIG 1-125
Sa | Ribosomal protein eS26 | RS26_PIG 1-115
Sb | Ribosomal protein eS27 | A0A287BF06_PIG 1-84
Sc | Ribosomal protein eS28 | RS28_PIG 1-69
Sd | Ribosomal protein uS14 | RS29_PIG 1-56
Se | Ribosomal protein eS30 | A0A480W155_PIG -73-59
Sf | Ribosomal protein eS31 | A0A4X1W6H9_PIG 1-156
Sg | Ribosomal protein RACK1 | RACK1_PIG 1-317
T | Ribosomal protein eL21 | RL21_PIG 1-160
U | Ribosomal protein eL22 | RL22_PIG 1-128
V | Ribosomal protein uL14 | A0A480VZZ1_PIG 1-140
W | Ribosomal protein eL24 | A0A4X1SH42_PIG 1-157
X | Ribosomal protein uL23 | A0A480KZ98_PIG 1-156
Y | Ribosomal protein uL24 | A0A4X1V977_PIG 1-145
Z | Ribosomal protein eL27 | RL27_PIG 1-136
a | Ribosomal protein uL15 | A0A4X1SN08_PIG 1-148
b | Ribosomal protein eL29 | RL29_PIG 1-160
c | Ribosomal protein eL30 | A0A4X1TXJ8_PIG 1-115
d | Ribosomal protein eL31 | RL31_PIG 1-125
e | Ribosomal protein eL32 | RL32_PIG 1-135
f | Ribosomal protein eL33 | A0A480KUB2_PIG 1-110
g | Ribosomal protein eL34 | RL34_PIG 1-117
h | Ribosomal protein uL29 | RL35_PIG 1-123
i | Ribosomal protein eL36 | A0A480QBP0_PIG 1-105
j | Ribosomal protein eL37 | A0A480UVT3_PIG 2-87
k | Ribosomal protein eL38 | F2Z568_PIG 1-70
l | Ribosomal protein eL39 | A0A4X1VIM4_PIG 1-51
m | Ribosomal protein eL40 | RL40_PIG 1-128
n | Ribosomal protein eL41 |
o | Ribosomal protein eL42 | A0A480LCM6_PIG 1-106
p | Ribosomal protein eL43 | A0A480WPS5_PIG 2-92
r | Ribosomal protein eL28 | A0A480YX24_PIG 2-126
z | Ribosomal protein uL1 | A0A480NYW2_PIG 1-217
Non-standard residues in 3j7r #5
---
MG — magnesium ion
ZN — zinc ion
> show sel cartoons
> hide sel atoms
> show sel cartoons
> hide sel atoms
> select subtract #4
Nothing selected
> select add #5
222336 atoms, 238785 bonds, 5347 pseudobonds, 18054 residues, 4 models
selected
> hide sel atoms
> show sel cartoons
> view matrix models #5,1,0,0,48.598,0,1,0,-19.462,0,0,1,-6.8603
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.94492,-0.32479,0.040421,145.62,0.32663,0.94366,-0.053117,-80.427,-0.020892,0.063394,0.99777,-18.475
> view matrix models
> #5,0.79865,-0.59472,0.09199,249.51,0.60144,0.79404,-0.088186,-105.2,-0.020598,0.12576,0.99185,-34.725
> view matrix models
> #5,0.54187,-0.067985,0.83771,-45.611,0.55997,0.77247,-0.29952,-25.818,-0.62675,0.6314,0.45665,147.62
> view matrix models
> #5,0.093891,0.61115,-0.78593,358.59,0.9823,0.071675,0.17308,-81.891,0.16211,-0.78827,-0.5936,636.61
> view matrix models
> #5,0.99544,0.079456,0.052735,11.767,0.030107,-0.78655,0.61679,305.14,0.090486,-0.61239,-0.78536,662.21
> view matrix models
> #5,0.22478,0.62395,-0.74844,306.92,0.96424,-0.031759,0.26312,-73.28,0.1404,-0.78082,-0.60878,645.04
> view matrix models
> #5,0.22979,0.62416,-0.74674,304.95,0.96318,-0.035781,0.26648,-72.802,0.13961,-0.78048,-0.6094,645.35
> view matrix models
> #5,-0.010133,-0.90075,-0.43422,719.49,0.83432,-0.24698,0.49287,-41.52,-0.55119,-0.35728,0.75401,323.35
> view matrix models
> #5,-0.29233,-0.8772,0.38088,555.73,0.863,-0.070368,0.50029,-102.46,-0.41205,0.47494,0.77759,38.346
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.29233,-0.8772,0.38088,514.24,0.863,-0.070368,0.50029,-83.627,-0.41205,0.47494,0.77759,86.547
> view matrix models
> #5,-0.29233,-0.8772,0.38088,400.87,0.863,-0.070368,0.50029,-127.27,-0.41205,0.47494,0.77759,-141.45
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.28815,0.025296,0.95725,-26.751,0.80021,0.55543,0.2262,-209.29,-0.52597,0.83118,-0.18029,67.138
> fitmap #5 inMap #1
Fit molecule 3j7r (#5) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1)
using 222336 atoms
average map value = 1.202, steps = 220
shifted from previous position = 111
rotated from previous position = 31.5 degrees
atoms outside contour = 15579, contour level = 0.15768
Position of 3j7r (#5) relative to cryosparc_P12_J230_001_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
-0.44298016 -0.45570532 0.77207593 321.80419538
0.67521627 0.39695181 0.62170110 -197.80941071
-0.58978943 0.79671948 0.13185787 191.79400298
Axis 0.09838873 0.76558934 0.63576145
Axis point 249.52586229 0.00000000 49.82519700
Rotation angle (degrees) 117.19918293
Shift along axis 2.15636446
> hide #!4 models
> show #!4 models
> hide #!5 models
> select #4/D
943 atoms, 957 bonds, 2 pseudobonds, 145 residues, 2 models selected
> select #3/Lm
419 atoms, 424 bonds, 4 pseudobonds, 53 residues, 2 models selected
> select #4/G
1055 atoms, 1070 bonds, 158 residues, 1 model selected
> hide #!4 models
> show #!5 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
> hide #!3 models
> volume #1 level 0.07485
> volume #1 level 0.1301
> volume #1 level 0.1945
> volume #1 level 0.1301
> hide #!4 models
> show #!5 models
> ui tool show "Side View"
> show #!2 models
> hide #!2 models
> show #!3 models
Mismatch between Cocoa 'c' and Carbon '\x0' for virtual key 8 with
QFlags(NoModifier)
Mismatch between Cocoa 'C' and Carbon '\x0' for virtual key 8 with
QFlags(ShiftModifier)
Mismatch between Cocoa 'c' and Carbon '\x0' for virtual key 8 with
QFlags(ControlModifier)
Mismatch between Cocoa 'c' and Carbon '\x0' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\u00e7' and Carbon '\x0' for virtual key 8 with
QFlags(AltModifier)
Mismatch between Cocoa '\u00c7' and Carbon '\x0' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\u00e7' and Carbon '\x0' for virtual key 8 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\u00c7' and Carbon '\x0' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> clip off
> show #!4 models
> hide #!5 models
Enter a PDB ID in the entry field
> open 7kai fromDatabase pdb format mmcif
7kai title:
Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with
Sec62, conformation 1 (C1) [more info...]
Chain information for 7kai #6
---
Chain | Description | UniProt
A | Protein transport protein SEC61 | SC61A_YEAST 1-480
B | Protein transport protein SBH1 | SC6B1_YEAST 1-82
C | Protein transport protein SSS1 | SC61G_YEAST 1-80
D | Protein translocation protein SEC63 | SEC63_YEAST 2-663
E | Translocation protein SEC66 | SEC66_YEAST 1-206
F | Translocation protein SEC72 | SEC72_YEAST 1-193
G | Protein transport protein Sec62 |
> select add #4
55482 atoms, 60473 bonds, 1730 pseudobonds, 3914 residues, 3 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> hide #!3 models
> show #!6 cartoons
> hide #!6 atoms
> ui mousemode right "translate selected models"
> select add #6
10718 atoms, 10924 bonds, 6 pseudobonds, 1399 residues, 2 models selected
> view matrix models #6,1,0,0,81.654,0,1,0,171.06,0,0,1,-24.225
> view matrix models #6,1,0,0,74.929,0,1,0,182.3,0,0,1,-29.163
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.61854,0.10391,-0.77886,227.87,0.61958,-0.67411,0.40212,297.63,-0.48325,-0.73129,-0.48134,373.09
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.61854,0.10391,-0.77886,99.303,0.61958,-0.67411,0.40212,281.31,-0.48325,-0.73129,-0.48134,279.3
> view matrix models
> #6,0.61854,0.10391,-0.77886,64.859,0.61958,-0.67411,0.40212,283.66,-0.48325,-0.73129,-0.48134,298.65
> view matrix models
> #6,0.61854,0.10391,-0.77886,74.869,0.61958,-0.67411,0.40212,280.8,-0.48325,-0.73129,-0.48134,314.77
> view matrix models
> #6,0.61854,0.10391,-0.77886,68.405,0.61958,-0.67411,0.40212,285.62,-0.48325,-0.73129,-0.48134,326.43
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.17002,-0.71875,-0.67416,252.35,0.26651,-0.62509,0.73365,283.66,-0.94872,-0.3044,0.085275,247.52
> view matrix models
> #6,0.074982,-0.90403,-0.42083,259.91,0.048092,-0.41825,0.90706,258.87,-0.99602,-0.088252,0.012116,230.73
> view matrix models
> #6,-0.15483,-0.94919,-0.27397,280.81,0.0010143,-0.27747,0.96073,235.85,-0.98794,0.14847,0.043923,187.22
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.15483,-0.94919,-0.27397,277.89,0.0010143,-0.27747,0.96073,236.43,-0.98794,0.14847,0.043923,182.39
> view matrix models
> #6,-0.15483,-0.94919,-0.27397,270.1,0.0010143,-0.27747,0.96073,238.94,-0.98794,0.14847,0.043923,195.63
> fitmap #6 inMap #1
Fit molecule 7kai (#6) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1)
using 10718 atoms
average map value = 1.233, steps = 128
shifted from previous position = 59.9
rotated from previous position = 35.7 degrees
atoms outside contour = 301, contour level = 0.13007
Position of 7kai (#6) relative to cryosparc_P12_J230_001_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
-0.10816285 -0.93883714 0.32693364 409.66306876
-0.02786266 0.33159671 0.94300969 148.09376535
-0.99374265 0.09288937 -0.06202495 406.02238554
Axis -0.46820539 0.72736499 0.50172093
Axis point 404.63507264 0.00000000 -52.82122007
Rotation angle (degrees) 114.79012046
Shift along axis 119.62169244
> undo
> show #!5 models
> select subtract #6
Nothing selected
> show #!4 models
> hide #!4 models
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select add #6
10718 atoms, 10924 bonds, 6 pseudobonds, 1399 residues, 2 models selected
> view matrix models
> #6,-0.15483,-0.94919,-0.27397,313.18,0.0010143,-0.27747,0.96073,207.82,-0.98794,0.14847,0.043923,131.47
> view matrix models
> #6,-0.15483,-0.94919,-0.27397,313.32,0.0010143,-0.27747,0.96073,207.01,-0.98794,0.14847,0.043923,131.06
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.14061,-0.92385,-0.356,318.9,0.40707,-0.38171,0.82981,180.97,-0.90251,-0.028238,0.42974,90.93
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.14061,-0.92385,-0.356,307.64,0.40707,-0.38171,0.82981,210.98,-0.90251,-0.028238,0.42974,137.86
> view matrix models
> #6,-0.14061,-0.92385,-0.356,282.89,0.40707,-0.38171,0.82981,199.96,-0.90251,-0.028238,0.42974,127.32
> view matrix models
> #6,-0.14061,-0.92385,-0.356,282.72,0.40707,-0.38171,0.82981,200.35,-0.90251,-0.028238,0.42974,127.17
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.25681,-0.90113,-0.34931,295.72,0.42003,-0.42958,0.7994,210.38,-0.87042,0.058569,0.48882,100
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,305.49,0.36901,-0.52549,0.76661,238.09,-0.88422,0.055622,0.46375,106.16
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,302.73,0.36901,-0.52549,0.76661,245.36,-0.88422,0.055622,0.46375,117.19
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,298.19,0.36901,-0.52549,0.76661,242.95,-0.88422,0.055622,0.46375,114.52
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,299.18,0.36901,-0.52549,0.76661,245.86,-0.88422,0.055622,0.46375,116.45
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,298.13,0.36901,-0.52549,0.76661,245.47,-0.88422,0.055622,0.46375,113.14
> fitmap #6 inMap #1
Fit molecule 7kai (#6) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1)
using 10718 atoms
average map value = 1.243, steps = 124
shifted from previous position = 79.8
rotated from previous position = 25 degrees
atoms outside contour = 206, contour level = 0.13007
Position of 7kai (#6) relative to cryosparc_P12_J230_001_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
-0.44566880 -0.88524978 -0.13308688 525.60779991
0.62690477 -0.41475890 0.65951909 183.49975684
-0.63903811 0.21049429 0.73981243 204.55973898
Axis -0.27105708 0.30542114 0.91282309
Axis point 248.72625582 218.26555113 0.00000000
Rotation angle (degrees) 124.07707591
Shift along axis 100.30183906
> undo
> hide #!5 models
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,298.8,0.36901,-0.52549,0.76661,246.79,-0.88422,0.055622,0.46375,116.85
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,300.74,0.36901,-0.52549,0.76661,250.37,-0.88422,0.055622,0.46375,116.98
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,295.03,0.36901,-0.52549,0.76661,248.6,-0.88422,0.055622,0.46375,122.82
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,295.39,0.36901,-0.52549,0.76661,247.22,-0.88422,0.055622,0.46375,119.89
> fitmap #6 inMap #1
Fit molecule 7kai (#6) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1)
using 10718 atoms
average map value = 1.252, steps = 132
shifted from previous position = 69.6
rotated from previous position = 14 degrees
atoms outside contour = 128, contour level = 0.13007
Position of 7kai (#6) relative to cryosparc_P12_J230_001_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
-0.50210231 -0.77701432 -0.37966038 551.57406813
0.29122789 -0.56528942 0.77177339 252.46983545
-0.81429698 0.27694151 0.51012137 250.18376402
Axis -0.39430287 0.34633674 0.85122036
Axis point 287.36516646 196.41254098 0.00000000
Rotation angle (degrees) 141.13578337
Shift along axis 82.91385494
> undo
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,291.09,0.36901,-0.52549,0.76661,250.51,-0.88422,0.055622,0.46375,128.28
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.65713,-0.73207,-0.17963,290.61,0.29854,-0.47157,0.82976,243.52,-0.69214,0.49163,0.52843,20.445
> view matrix models
> #6,-0.54642,-0.76733,-0.3356,301.86,0.21282,-0.51477,0.83049,263.27,-0.81002,0.38237,0.44459,67.727
> fitmap #6 inMap #1
Fit molecule 7kai (#6) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1)
using 10718 atoms
average map value = 1.283, steps = 132
shifted from previous position = 73.9
rotated from previous position = 43.2 degrees
atoms outside contour = 145, contour level = 0.13007
Position of 7kai (#6) relative to cryosparc_P12_J230_001_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
-0.56048648 -0.77324597 -0.29655616 522.99378216
0.71208631 -0.63279811 0.30413748 258.45120363
-0.42283327 -0.04070863 0.90529267 195.50461904
Axis -0.22538111 0.08253094 0.97076877
Axis point 224.09082246 251.30323054 0.00000000
Rotation angle (degrees) 130.09043809
Shift along axis 93.24708045
> undo
> volume #1 level 0.07485
> fitmap #6 inMap #1
Fit molecule 7kai (#6) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1)
using 10718 atoms
average map value = 1.269, steps = 116
shifted from previous position = 77.5
rotated from previous position = 9.05 degrees
atoms outside contour = 157, contour level = 0.074854
Position of 7kai (#6) relative to cryosparc_P12_J230_001_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
-0.67920128 -0.72835307 -0.09048420 536.37887288
0.42277926 -0.48903191 0.76295836 218.05786119
-0.59995274 0.47994746 0.64008369 169.44235071
Axis -0.21934487 0.39485867 0.89217401
Axis point 254.00802490 186.84176094 0.00000000
Rotation angle (degrees) 139.82474868
Shift along axis 119.62214637
> undo
> show #!5 models
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.28634,-0.84898,-0.44412,273.5,0.36901,-0.52549,0.76661,231.44,-0.88422,0.055622,0.46375,24.349
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.79561,-0.51975,0.31124,189.7,0.46231,-0.18888,0.86637,149.36,-0.39151,0.83318,0.39056,-163.62
> view matrix models
> #6,-0.33373,-0.88323,-0.32943,269.67,0.45285,-0.45671,0.76573,207.91,-0.82677,0.10636,0.55239,-5.1508
> volume #1 level 0.489
> view matrix models
> #6,-0.21804,-0.82307,-0.52441,270.56,0.47699,-0.55867,0.67851,233.03,-0.85143,-0.1022,0.51441,37.268
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.21804,-0.82307,-0.52441,283.38,0.47699,-0.55867,0.67851,247.89,-0.85143,-0.1022,0.51441,130.88
> view matrix models
> #6,-0.21804,-0.82307,-0.52441,294.76,0.47699,-0.55867,0.67851,245.27,-0.85143,-0.1022,0.51441,121.54
> view matrix models
> #6,-0.21804,-0.82307,-0.52441,295.18,0.47699,-0.55867,0.67851,245.43,-0.85143,-0.1022,0.51441,126.7
> view matrix models
> #6,-0.21804,-0.82307,-0.52441,295.43,0.47699,-0.55867,0.67851,245.08,-0.85143,-0.1022,0.51441,127.46
> view matrix models
> #6,-0.21804,-0.82307,-0.52441,295.72,0.47699,-0.55867,0.67851,245.21,-0.85143,-0.1022,0.51441,128.06
> volume #1 level 0.07485
> hide #!5 models
> show #!5 models
> hide #!6 models
> select subtract #6
Nothing selected
> show #!4 models
> hide #!5 models
> volume #1 level 0.1669
> hide #!4 models
> hide #!1 models
> show #!6 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui mousemode right "rotate selected models"
> select add #6
10718 atoms, 10924 bonds, 6 pseudobonds, 1399 residues, 2 models selected
> view matrix models
> #6,-0.0055515,-0.95806,-0.28652,250.94,0.41205,-0.26326,0.8723,180.15,-0.91114,-0.11322,0.39623,155.82
> undo
> show #!5 models
> hide #!6 models
> select subtract #6
Nothing selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
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 Pro
Model Identifier: Mac14,7
Model Number: Z16U000NJD/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 44 days, 19 hours, 36 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P3223QE:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.5
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
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
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
pycollada: 0.8
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
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_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 , 3 months 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 , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel explained 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 thought this was fixed by Qt 6.8.2 in ChimeraX 1.10 but apparently it is not fixed. We are now using Qt 6.9.1 in ChimeraX daily builds so you might try that to avoid these Mac multi-display crashes.
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Reported by Ahn Nguyen