![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18385 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: 1.9 (2024-12-11 19:11:19 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: Segmentation fault
Current thread 0x0000000204b08c80 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 56)
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{
"uptime" : 1100000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 10309,
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"build" : "24E263",
"releaseType" : "User"
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"captureTime" : "2025-08-07 12:48:21.6553 +0200",
"codeSigningMonitor" : 1,
"incident" : "A47F65A3-E24B-4CCD-839D-9A114A1D07CF",
"pid" : 21474,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-07 10:38:57.7199 +0200",
"procStartAbsTime" : 27174557212824,
"procExitAbsTime" : 27306887443339,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"2A3E354F-F384-55C6-9585-9D87CCE7E68B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D9CE6AD1-DD38-1AD7-DD6F-C8D74DC2AAA2",
"appleIntelligenceStatus" : {"reasons":["notOptedIn"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "18FC82E7-CDA4-4908-8D84-1C8490883140",
"wakeTime" : 3,
"sleepWakeUUID" : "A6AE4EBF-20A8-4AEB-A3B1-DD2D72CAE254",
"sip" : "enabled",
"vmRegionInfo" : "0x5d04d9c6e108 is not in any region. Bytes after previous region: 101794378604809 Bytes before following region: 3277701324536\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000dd04d9c6e108","rawCodes":[1,243012903297288],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000dd04d9c6e108 -> 0x00005d04d9c6e108 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":21474},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x5d04d9c6e108 is not in any region. Bytes after previous region: 101794378604809 Bytes before following region: 3277701324536\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/M_maps/MSR-050825/species/0fe51d64/coldshock_canonHiber_filt.mrc
Opened coldshock_canonHiber_filt.mrc as #1, grid size 232,232,232, pixel 2.59,
shown at level 0.00651, step 1, values float32
> open
> /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/M_maps/MSR-050825/species/2f5041e5/coldshock_CDwithoutBalon_filt.mrc
Opened coldshock_CDwithoutBalon_filt.mrc as #2, grid size 270,270,270, pixel
2.59, shown at level 0.00734, step 2, values float32
> open
> /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/M_maps/MSR-050825/species/8d822ac8/coldshock_noncanonHiber_filt.mrc
Opened coldshock_noncanonHiber_filt.mrc as #3, grid size 232,232,232, pixel
2.59, shown at level 0.00408, step 1, values float32
> open
> /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/M_maps/MSR-050825/species/eb6b5fa6/coldshock_CDcolliding_filt.mrc
Opened coldshock_CDcolliding_filt.mrc as #4, grid size 270,270,270, pixel
2.59, shown at level 0.00718, step 2, values float32
> open
> /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/M_maps/MSR-050825/species/f27bc761/coldshock_CDwithBalon_filt.mrc
Opened coldshock_CDwithBalon_filt.mrc as #5, grid size 270,270,270, pixel
2.59, shown at level 0.00736, step 2, values float32
> hide #!5 models
> hide #!4 models
> hide #!2 models
> volume #3 level 0.003637
> volume #3 level 0.003397
> volume #3 level 0.003774
> volume #1 level 0.00402
> volume #1 level 0.006047
> volume #1 level 0.004573
> volume #1 level 0.003836
> volume #1 level 0.004481
> volume #2 level 0.0043
> volume #4 level 0.005212
> volume #4 level 0.004387
> volume #5 level 0.004957
> volume #5 level 0.003779
> volume #5 level 0.004912
> volume #1 level 0.003698
> volume #1 level 0.003513
> open 8rdv fromDatabase pdb format mmcif
8rdv title:
Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation
factor Balon, mRNA and P-site tRNA (structure 2). [more info...]
Chain information for 8rdv #6
---
Chain | Description | UniProt
A4 | Small ribosomal subunit protein uS2 | A0A0M4TFJ4_9GAMM 1-269
Af | Large ribosomal subunit protein uL3 | A0A0M4T1M3_9GAMM 1-212
B | Methyl-accepting chemotaxis protein | A0A0M3V8U3_9GAMM 1-369
BQ | Small ribosomal subunit protein uS8 | A0A0M4U618_9GAMM 1-132
Ba | Large ribosomal subunit protein bL34 | A0A0M4TEZ6_9GAMM 1-44
C1 | Large ribosomal subunit protein bL9 | A0A0M3V9E8_9GAMM 1-166
CT | Small ribosomal subunit protein uS3 | A0A0M4T6V9_9GAMM 1-241
Cl | Large ribosomal subunit protein uL2 | A0A0M3V8Q0_9GAMM 1-274
D8 | 5S rRNA |
Dm | Small ribosomal subunit protein uS4 | A0A0M4TE52_9GAMM 1-213
E5 | Small ribosomal subunit protein uS5 | A0A0M3V8J0_9GAMM 1-171
E9 | Large ribosomal subunit protein uL4 | A0A0M4U627_9GAMM 1-200
F | Small ribosomal subunit protein uS9 | A0A0M4T6M9_9GAMM 1-128
F7 | Large ribosomal subunit protein uL5 | A0A0M4T1L5_9GAMM 1-178
FG | Small ribosomal subunit protein bS6 | A0A0M4U628_9GAMM 1-134
GR | Large ribosomal subunit protein uL6 | A0A0M5MKV2_9GAMM 1-177
GS | Small ribosomal subunit protein uS7 | A0A0M3V8N5_9GAMM 1-157
H | Elongation factor Tu | A0A0M4U5B4_9GAMM 1-396
HK | Small ribosomal subunit protein uS14 | A0A0M3V8P8_9GAMM 1-101
IX | Large ribosomal subunit protein uL13 | A0A0M4TBP4_9GAMM 1-142
JY | Small ribosomal subunit protein uS10 | A0A0M4TE68_9GAMM 1-103
Je | Large ribosomal subunit protein uL14 | A0A0M5MJS2_9GAMM 1-122
KU | Small ribosomal subunit protein uS11 | A0A0M3V8P6_9GAMM 1-129
Kd | Large ribosomal subunit protein uL15 | A0A0M4T6V1_9GAMM 1-146
L6 | Small ribosomal subunit protein uS12 | A0A0M4U4C3_9GAMM 1-124
Lg | Large ribosomal subunit protein uL16 | A0A0M3V8J3_9GAMM 1-137
MB | Large ribosomal subunit protein bL17 | A0A0M4U611_9GAMM 1-119
MM | Small ribosomal subunit protein uS13 | A0A0M5MJL8_9GAMM 1-118
NV | Small ribosomal subunit protein bS21 | A0A0M4SY21_9GAMM 1-71
Nc | Large ribosomal subunit protein uL18 | A0A0M4TUJ2_9GAMM 1-116
OL | Small ribosomal subunit protein uS15 | A0A0M4TF29_9GAMM 1-88
Oi | Large ribosomal subunit protein bL19 | A0A0M4TV08_9GAMM 1-130
PO | Large ribosomal subunit protein bL20 | A0A0M5MJR6_9GAMM 1-118
Pj | Small ribosomal subunit protein bS16 | A0A0M4T275_9GAMM 1-89
QZ | Small ribosomal subunit protein uS17 | A0A0M4U401_9GAMM 1-91
Qb | Large ribosomal subunit protein bL21 | A0A0M5TIS3_9GAMM 1-103
R3 | Small ribosomal subunit protein bS18 | A0A0M5MK69_9GAMM 1-76
RF | Large ribosomal subunit protein uL22 | A0A0M4SWS6_9GAMM 1-109
SP | Small ribosomal subunit protein uS19 | A0A0M4TUJ8_9GAMM 1-91
Sn | Large ribosomal subunit protein uL23 | A0A0M5MJH9_9GAMM 1-116
TI | Large ribosomal subunit protein uL24 | A0A0M4TE60_9GAMM 1-105
To | Small ribosomal subunit protein bS20 | A0A0M4T3R2_9GAMM 1-88
UC | Large ribosomal subunit protein bL25 | A0A0M4U726_9GAMM 1-219
V | Heterogenous tRNA |
VH | Large ribosomal subunit protein bL27 | A0A0M4TUE5_9GAMM 1-85
WD | Large ribosomal subunit protein bL28 | A0A0M4T6Y7_9GAMM 1-78
XE | Large ribosomal subunit protein uL29 | A0A0M4TBX9_9GAMM 1-65
Y | Heterogenous mRNA |
YW | Large ribosomal subunit protein uL30 | A0A0M4SWR7_9GAMM 1-59
Z2 | 23S rRNA |
aA | Large ribosomal subunit protein bL32 | A0A0M4SWQ6_9GAMM 1-60
bk | Large ribosomal subunit protein bL33 | A0A0M4SWV1_9GAMM 1-51
dh | Large ribosomal subunit protein bL35 | A0A0M4U4I0_9GAMM 1-65
ep | Large ribosomal subunit protein bL36 | A0A0M4U3Z5_9GAMM 1-38
fJ | Large ribosomal subunit protein bL31B | A0A0M4SX87_9GAMM 1-93
iN | 16S rRNA |
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #6
142059 atoms, 154016 bonds, 4467 pseudobonds, 10507 residues, 3 models
selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,215.56,0,1,0,1.8946,0,0,1,74.466
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.95489,-0.291,-0.059171,290.09,0.29542,0.91065,0.28886,-95.856,-0.030174,-0.29331,0.95554,143.63
> view matrix models
> #6,0.94197,-0.30307,0.14432,253.41,0.25615,0.92684,0.27451,-88.549,-0.21696,-0.22161,0.95069,166.48
> view matrix models
> #6,0.96869,0.14338,0.20267,153.65,-0.20929,0.91075,0.35599,-14.47,-0.13354,-0.38727,0.91225,189.33
> view matrix models
> #6,0.98296,0.16668,0.077495,172.08,-0.18357,0.9118,0.36732,-21.81,-0.0094369,-0.37529,0.92686,160.77
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.98296,0.16668,0.077495,46.378,-0.18357,0.9118,0.36732,0.46417,-0.0094369,-0.37529,0.92686,226.2
> view matrix models
> #6,0.98296,0.16668,0.077495,24.772,-0.18357,0.9118,0.36732,73.732,-0.0094369,-0.37529,0.92686,225.79
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99682,0.077536,0.018407,50.717,-0.079351,0.94442,0.31903,57.864,0.0073523,-0.31947,0.94757,208.06
> view matrix models
> #6,0.96567,0.21901,0.1397,5.6733,-0.2174,0.97571,-0.026882,148.35,-0.14219,-0.0044106,0.98983,169.15
> view matrix models
> #6,0.97204,0.18697,0.14208,9.9379,-0.18592,0.98235,-0.020733,139.94,-0.14345,-0.0062618,0.98964,169.77
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.97204,0.18697,0.14208,44.909,-0.18592,0.98235,-0.020733,134.98,-0.14345,-0.0062618,0.98964,156.38
> ui tool show "Fit in Map"
> fitmap #6 inMap #1
Fit molecule 8rdv (#6) to map coldshock_canonHiber_filt.mrc (#1) using 142059
atoms
average map value = 0.008669, steps = 100
shifted from previous position = 14
rotated from previous position = 11 degrees
atoms outside contour = 3433, contour level = 0.0035132
Position of 8rdv (#6) relative to coldshock_canonHiber_filt.mrc (#1)
coordinates:
Matrix rotation and translation
0.99900134 0.03551027 0.02711709 92.10578523
-0.03521318 0.99931530 -0.01135620 109.53736959
-0.02750178 0.01038998 0.99956776 117.85837821
Axis 0.23645643 0.59389657 -0.76900925
Axis point 3223.96809613 -2528.42295718 0.00000000
Rotation angle (degrees) 2.63558909
Shift along axis -3.80130908
> select subtract #6
Nothing selected
> fitmap #6 inMap #3
Fit molecule 8rdv (#6) to map coldshock_noncanonHiber_filt.mrc (#3) using
142059 atoms
average map value = 0.005992, steps = 44
shifted from previous position = 0.078
rotated from previous position = 0.0748 degrees
atoms outside contour = 20304, contour level = 0.0037738
Position of 8rdv (#6) relative to coldshock_noncanonHiber_filt.mrc (#3)
coordinates:
Matrix rotation and translation
0.99896294 0.03558325 0.02840567 91.76464938
-0.03527833 0.99931516 -0.01116458 109.48473981
-0.02878349 0.01015089 0.99953413 118.16990151
Axis 0.22791996 0.61150666 -0.75770185
Axis point 3180.90669206 -2496.87444205 0.00000000
Rotation angle (degrees) 2.68017736
Shift along axis -1.67191103
> show #!3 models
> hide #!1 models
> volume #3 level 0.002918
> color #6 grey
> select add #6
142059 atoms, 154016 bonds, 4467 pseudobonds, 10507 residues, 3 models
selected
> select /B
2829 atoms, 2870 bonds, 1 pseudobond, 362 residues, 2 models selected
> color sel #D62828
> hide #!6 models
> hide #!3 models
> show #!6 models
> color /V #08A8C6
> color /H #FCBF49
> select clear
> select add #6
142059 atoms, 154016 bonds, 4467 pseudobonds, 10507 residues, 3 models
selected
> select subtract /B:272
142050 atoms, 154006 bonds, 4467 pseudobonds, 10506 residues, 3 models
selected
> select subtract /B:273
142042 atoms, 153998 bonds, 4467 pseudobonds, 10505 residues, 3 models
selected
> color #6 #D3D3D3
> color /H #FCBF49
> color /V #08A8C6
> select clear
> select /B
2829 atoms, 2870 bonds, 1 pseudobond, 362 residues, 2 models selected
> color sel #D62828
> select clear
> show #!3 models
> volume #3 level 0.002371
> volume #3 level 0.004048
> open 8rdw fromDatabase pdb format mmcif
8rdw title:
Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation
factor Balon and EF-Tu(GDP) (structure 3). [more info...]
Chain information for 8rdw #7
---
Chain | Description | UniProt
A4 | Small ribosomal subunit protein uS2 | A0A0M4TFJ4_9GAMM 1-269
Af | Large ribosomal subunit protein uL3 | A0A0M4T1M3_9GAMM 1-212
B | Methyl-accepting chemotaxis protein | A0A0M3V8U3_9GAMM 1-369
BQ | Small ribosomal subunit protein uS8 | A0A0M4U618_9GAMM 1-132
Ba | Large ribosomal subunit protein bL34 | A0A0M4TEZ6_9GAMM 1-44
C1 | Large ribosomal subunit protein bL9 | A0A0M3V9E8_9GAMM 1-166
CT | Small ribosomal subunit protein uS3 | A0A0M4T6V9_9GAMM 1-241
Cl | Large ribosomal subunit protein uL2 | A0A0M3V8Q0_9GAMM 1-274
D | Large ribosomal subunit protein bL12 | A0A0M4SX69_9GAMM 1-123
D8 | 5S rRNA |
Dm | Small ribosomal subunit protein uS4 | A0A0M4TE52_9GAMM 1-213
E5 | Small ribosomal subunit protein uS5 | A0A0M3V8J0_9GAMM 1-171
E9 | Large ribosomal subunit protein uL4 | A0A0M4U627_9GAMM 1-200
F | Small ribosomal subunit protein uS9 | A0A0M4T6M9_9GAMM 1-128
F7 | Large ribosomal subunit protein uL5 | A0A0M4T1L5_9GAMM 1-178
FG | Small ribosomal subunit protein bS6 | A0A0M4U628_9GAMM 1-134
GR | Large ribosomal subunit protein uL6 | A0A0M5MKV2_9GAMM 1-177
GS | Small ribosomal subunit protein uS7 | A0A0M3V8N5_9GAMM 1-157
H | Elongation factor Tu | A0A0M4U5B4_9GAMM 1-396
HK | Small ribosomal subunit protein uS14 | A0A0M3V8P8_9GAMM 1-101
IX | Large ribosomal subunit protein uL13 | A0A0M4TBP4_9GAMM 1-142
JY | Small ribosomal subunit protein uS10 | A0A0M4TE68_9GAMM 1-103
Je | Large ribosomal subunit protein uL14 | A0A0M5MJS2_9GAMM 1-122
KU | Small ribosomal subunit protein uS11 | A0A0M3V8P6_9GAMM 1-129
Kd | Large ribosomal subunit protein uL15 | A0A0M4T6V1_9GAMM 1-146
L6 | Small ribosomal subunit protein uS12 | A0A0M4U4C3_9GAMM 1-124
Lg | Large ribosomal subunit protein uL16 | A0A0M3V8J3_9GAMM 1-137
MB | Large ribosomal subunit protein bL17 | A0A0M4U611_9GAMM 1-119
MM | Small ribosomal subunit protein uS13 | A0A0M5MJL8_9GAMM 1-118
NV | Small ribosomal subunit protein bS21 | A0A0M4SY21_9GAMM 1-71
Nc | Large ribosomal subunit protein uL18 | A0A0M4TUJ2_9GAMM 1-116
OL | Small ribosomal subunit protein uS15 | A0A0M4TF29_9GAMM 1-88
Oi | Large ribosomal subunit protein bL19 | A0A0M4TV08_9GAMM 1-130
PO | Large ribosomal subunit protein bL20 | A0A0M5MJR6_9GAMM 1-118
Pj | Small ribosomal subunit protein bS16 | A0A0M4T275_9GAMM 1-89
QZ | Small ribosomal subunit protein uS17 | A0A0M4U401_9GAMM 1-91
Qb | Large ribosomal subunit protein bL21 | A0A0M5TIS3_9GAMM 1-103
R3 | Small ribosomal subunit protein bS18 | A0A0M5MK69_9GAMM 1-76
RF | Large ribosomal subunit protein uL22 | A0A0M4SWS6_9GAMM 1-109
SP | Small ribosomal subunit protein uS19 | A0A0M4TUJ8_9GAMM 1-91
Sn | Large ribosomal subunit protein uL23 | A0A0M5MJH9_9GAMM 1-116
TI | Large ribosomal subunit protein uL24 | A0A0M4TE60_9GAMM 1-105
To | Small ribosomal subunit protein bS20 | A0A0M4T3R2_9GAMM 1-88
UC | Large ribosomal subunit protein bL25 | A0A0M4U726_9GAMM 1-219
VH | Large ribosomal subunit protein bL27 | A0A0M4TUE5_9GAMM 1-85
WD | Large ribosomal subunit protein bL28 | A0A0M4T6Y7_9GAMM 1-78
XE | Large ribosomal subunit protein uL29 | A0A0M4TBX9_9GAMM 1-65
YW | Large ribosomal subunit protein uL30 | A0A0M4SWR7_9GAMM 1-59
Z2 | 23S rRNA |
aA | Large ribosomal subunit protein bL32 | A0A0M4SWQ6_9GAMM 1-60
bk | Large ribosomal subunit protein bL33 | A0A0M4SWV1_9GAMM 1-51
dh | Large ribosomal subunit protein bL35 | A0A0M4U4I0_9GAMM 1-65
ep | Large ribosomal subunit protein bL36 | A0A0M4U3Z5_9GAMM 1-38
fJ | Large ribosomal subunit protein bL31B | A0A0M4SX87_9GAMM 1-93
iN | 16S rRNA |
Non-standard residues in 8rdw #7
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #7
142682 atoms, 154557 bonds, 4425 pseudobonds, 10699 residues, 4 models
selected
> hide sel atoms
> show sel cartoons
> view matrix models #7,1,0,0,182.59,0,1,0,-21.711,0,0,1,18.146
> view matrix models #7,1,0,0,182.74,0,1,0,-23.828,0,0,1,8.9496
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.9131,0.10227,0.39469,99.941,-0.07888,0.99405,-0.075078,7.2713,-0.40003,0.037421,0.91574,93.967
> view matrix models
> #7,0.76653,-0.37929,0.51824,191.73,0.49034,0.86678,-0.090887,-72.429,-0.41473,0.32378,0.85039,56.804
> view matrix models
> #7,0.86493,0.19523,0.46237,77.967,-0.22602,0.97405,0.011516,20.957,-0.44812,-0.11446,0.88661,137.08
> view matrix models
> #7,0.98502,0.14956,0.085873,140.35,-0.1571,0.98357,0.088909,-9.4113,-0.071165,-0.10107,0.99233,42.591
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.98502,0.14956,0.085873,44.567,-0.1571,0.98357,0.088909,33.149,-0.071165,-0.10107,0.99233,169.83
> view matrix models
> #7,0.98502,0.14956,0.085873,26.43,-0.1571,0.98357,0.088909,99.993,-0.071165,-0.10107,0.99233,175.82
> view matrix models
> #7,0.98502,0.14956,0.085873,61.355,-0.1571,0.98357,0.088909,95.57,-0.071165,-0.10107,0.99233,160.38
> view matrix models
> #7,0.98502,0.14956,0.085873,61.65,-0.1571,0.98357,0.088909,95.316,-0.071165,-0.10107,0.99233,157.17
> fitmap #7 inMap #3
Fit molecule 8rdw (#7) to map coldshock_noncanonHiber_filt.mrc (#3) using
142682 atoms
average map value = 0.00596, steps = 92
shifted from previous position = 21.7
rotated from previous position = 9.69 degrees
atoms outside contour = 26538, contour level = 0.0040475
Position of 8rdw (#7) relative to coldshock_noncanonHiber_filt.mrc (#3)
coordinates:
Matrix rotation and translation
0.99916956 0.03241120 0.02469236 93.24986343
-0.03220587 0.99944366 -0.00866862 108.41335331
-0.02495958 0.00786619 0.99965751 118.03237077
Axis 0.19885295 0.59713013 -0.77710560
Axis point 3571.83042084 -2837.37460473 0.00000000
Rotation angle (degrees) 2.38278595
Shift along axis -8.44372641
> select subtract #7
Nothing selected
> hide #!6 models
> volume #3 level 0.004492
> volume #3 level 0.004048
> show #!6 models
> hide #!7 models
> ui tool show "Surface Color"
> ui tool show "Color Zone"
> color zone #3 near #6 distance 15.53
> color zone #3 near #6 distance 15.4
> color zone #3 near #6 distance 4.87
> color zone #3 near #6 distance 4.52
> color zone #3 near #6 distance 6.08
> hide #!3 models
> show #!3 models
> color zone #3 near #6 distance 9.68
> color zone #3 near #6 distance 6.93
> color zone #3 near #6 distance 47.77
> color zone #3 near #6 distance 5
> color zone #3 near #6 distance 50
> color zone #3 near #7 distance 48.67
> color zone #3 near #7 distance 30.03
> color zone #3 near #6 distance 30.03
> color zone #3 near #6 distance 15.03
> volume #3 level 0.003568
> volume #3 level 0.002439
> volume #3 level 0.002747
> volume #3 level 0.002884
> volume #3 level 0.003363
> volume #3 level 0.003124
> volume splitbyzone #3
Opened coldshock_noncanonHiber_filt.mrc 0 as #8.1, grid size 232,232,232,
pixel 2.59, shown at level 0.00312, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 1 as #8.2, grid size 232,232,232,
pixel 2.59, shown at level 0.00312, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 2 as #8.3, grid size 232,232,232,
pixel 2.59, shown at level 0.00312, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 3 as #8.4, grid size 232,232,232,
pixel 2.59, shown at level 0.00312, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 4 as #8.5, grid size 232,232,232,
pixel 2.59, shown at level 0.00312, step 1, values float32
> ui tool show "Fit in Map"
> hide #!8 models
> show #!7 models
> hide #!6 models
> color #7 #D3D3D3
> select #7/B:251
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
2871 atoms, 2914 bonds, 368 residues, 1 model selected
> color sel #D62828
> select #7/H:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
99 atoms, 102 bonds, 12 residues, 1 model selected
> select up
2918 atoms, 2968 bonds, 386 residues, 1 model selected
> select up
2947 atoms, 2998 bonds, 388 residues, 1 model selected
> select up
142682 atoms, 154557 bonds, 10699 residues, 1 model selected
> select down
2947 atoms, 2998 bonds, 388 residues, 1 model selected
> color sel #FCBF49
> fitmap #7 inMap #3
Fit molecule 8rdw (#7) to map coldshock_noncanonHiber_filt.mrc (#3) using
142682 atoms
average map value = 0.00596, steps = 40
shifted from previous position = 0.026
rotated from previous position = 0.0197 degrees
atoms outside contour = 10980, contour level = 0.0031235
Position of 8rdw (#7) relative to coldshock_noncanonHiber_filt.mrc (#3)
coordinates:
Matrix rotation and translation
0.99917339 0.03239976 0.02455170 93.27698067
-0.03220330 0.99944641 -0.00835559 108.34749174
-0.02480882 0.00755804 0.99966364 118.03603866
Axis 0.19208976 0.59581921 -0.77980831
Axis point 3590.48202106 -2844.08965597 0.00000000
Rotation angle (degrees) 2.37400788
Shift along axis -9.57241428
> show #!8 models
> hide #!8 models
> show #!3 models
> volume #8.1 level 0.003303
> volume #3 level 0.004903
> volume #3 level 0.004048
> volume #3 level 0.00374
> color zone #3 near #7 distance 15.03
> color zone #3 near #7 distance 3
> color zone #3 near #7 distance 30
> color zone #3 near #7 distance 3
> color zone #3 near #7 distance 4
> color zone #3 near #7 distance 45
> color zone #3 near #7 distance 4
> color zone #3 near #7 distance 6
> color zone #3 near #7 distance 60
> volume splitbyzone #3
Opened coldshock_noncanonHiber_filt.mrc 0 as #9.1, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 1 as #9.2, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 2 as #9.3, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 3 as #9.4, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
> view matrix models
> #7,0.99917,0.0324,0.024552,94.63,-0.032203,0.99945,-0.0083556,108.29,-0.024809,0.007558,0.99966,121.28
> fitmap #7 inMap #3
Fit molecule 8rdw (#7) to map coldshock_noncanonHiber_filt.mrc (#3) using
142682 atoms
average map value = 0.00596, steps = 52
shifted from previous position = 3.5
rotated from previous position = 0.00828 degrees
atoms outside contour = 20361, contour level = 0.0037395
Position of 8rdw (#7) relative to coldshock_noncanonHiber_filt.mrc (#3)
coordinates:
Matrix rotation and translation
0.99917264 0.03238693 0.02459927 93.27284194
-0.03219349 0.99944786 -0.00821955 108.32264072
-0.02485190 0.00742081 0.99966360 118.08633635
Axis 0.18882681 0.59702609 -0.77968217
Axis point 3595.01414754 -2845.16973281 0.00000000
Rotation angle (degrees) 2.37355959
Shift along axis -9.78595401
> close #1
> close #2
> close #4
> close #5
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!8.1 models
> show #!8.1 models
> color #8.1 #D3D3D3
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!8 models
> select clear
> show #!3 models
> hide #!9.1 models
> show #!9 models
> hide #!9 models
> hide #!7 models
> hide #!3 models
> show #!3 models
> color #3 #D3D3D3
> hide #!3 models
> show #!6 models
> show #!3 models
> show #!7 models
> ui tool show "Color Zone"
> color zone #3 near #6 distance 15.53
> color zone #3 near #6 distance 4.53
> color zone #3 near #6 distance 45.53
> color zone #3 near #6 distance 4.53
> color zone #3 near #6 distance 3.53
> color zone #3 near #6 distance 30.53
> hide #!3 models
> show #!3 models
> color zone #3 near #6 distance 3.53
> color zone #3 near #6 distance 15.53
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> volume splitbyzone #3
Opened coldshock_noncanonHiber_filt.mrc 0 as #1.1, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 1 as #1.2, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 2 as #1.3, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 3 as #1.4, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 4 as #1.5, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> select add #1.1
2 models selected
> color zone #1.1 near #7 distance 15.53
> select clear
> color #1.1 #D3D3D3
> color #1.3 #D3D3D3
> hide #!6 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> set bgColor white
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> material
Reflectivity: 0.8
Specular reflectivity 0.3
Specular exponent: 30
Ambient reflectivity 0.8
Transparent cast shadows: false
Meshes cast shadows: false
> material
Reflectivity: 0.8
Specular reflectivity 0.3
Specular exponent: 30
Ambient reflectivity 0.8
Transparent cast shadows: false
Meshes cast shadows: false
> material dull
> material
Reflectivity: 0.8
Specular reflectivity 0
Specular exponent: 30
Ambient reflectivity 0.8
Transparent cast shadows: false
Meshes cast shadows: false
> graphics
Background color: 100,100,100
> lighting
Intensity: 0.5
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 1.5
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01)
> lighting intensity 0.7
> lighting fill intensity 0.3
Expected keyword "fillColor", "fillDirection", or "fillIntensity"
> lighting fillIntensity 0.3
> lighting
Intensity: 0.7
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0.3
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 1.5
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01)
> lighting ambientIntensity 0.8
> lighting depthCue true
> lighting
Intensity: 0.7
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0.3
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 0.8
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01)
> material
Reflectivity: 0.8
Specular reflectivity 0
Specular exponent: 30
Ambient reflectivity 0.8
Transparent cast shadows: false
Meshes cast shadows: false
> graphics silhouettes
Current silhouette settings:
enabled: True
width: 2
color: 0,0,0
depth jump: 0.03
> graphics silhouettes width 4
> graphics silhouettes
Current silhouette settings:
enabled: True
width: 4
color: 0,0,0
depth jump: 0.03
> save
> /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/FigurePrep_manuskript/Figure3_noncanonHiber.cxs
> includeMaps true
> volume #3 level 0.004082
> volume #3 level 0.005177
> volume #3 level 0.004082
> volume #3 level 0.004
> volume #3 level 0.005
> volume #3 level 0.0045
> volume #3 level 0.006
> volume #3 level 0.003
> volume #3 level 0.0035
> volume #3 level 0.0030
> volume #3 level 0.0038
> volume #3 level 0.004
> volume #3 level 0.0042
> volume #3 level 0.0040
> volume #3 level 0.0047
> volume #3 level 0.0038
> show #!6 models
> volume #3 level 0.0040
> volume #3 level 0.0045
> volume #3 level 0.0035
> volume #3 level 0.0033
> volume #3 level 0.0040
> volume #3 level 0.0038
> hide #!6 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9.2 models
> hide #!9.3 models
> hide #!9.4 models
> show #!9.4 models
> hide #!9.4 models
> show #!9.4 models
> hide #!9.4 models
> show #!9.4 models
> hide #!9.4 models
> show #!9.4 models
> hide #!9.4 models
> show #!9.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> hide #!1 models
> volume #9.4 level 0.0038
> hide #!9.4 models
> show #!9.4 models
> hide #!9.4 models
> show #!9.4 models
> ui tool show "Side View"
Need to color zone map before it can be split
> show #!1.4 models
> hide #!1.4 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> hide #!1.3 models
> hide #!9 models
> show #!9 models
> hide #!1.2 models
> show #!1.2 models
> show #!9.2 models
> hide #!9.2 models
> show #!8 models
> hide #!8 models
> hide #!3 models
> show #!1.3 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1 models
> show #!8 models
> hide #!8.3 models
> show #!8.3 models
> hide #!8.1 models
> show #!8.1 models
> hide #!8.1 models
> show #!8.1 models
> show #!1 models
> hide #!8 models
> hide #!9 models
> show #!1.2 models
> show #!1.4 models
> show #!1.1 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!9.2 models
> show #!9.3 models
> show #!9.1 models
> hide #!9.1 models
> show #!9.1 models
> hide #!9.1 models
> show #!9.1 models
> hide #!9.1 models
> hide #!9.3 models
> show #!9.3 models
> hide #!8.5 models
> show #!8.5 models
> hide #!8.1 models
> hide #!8.3 models
> hide #!8.2 models
> hide #!8.4 models
> show #!8.4 models
> hide #!8.4 models
> volume #8.4 level 0.0038
> hide #!9.3 models
> show #!9.3 models
> hide #!8 models
> show #!8 models
> hide #!9.3 models
> show #!9.3 models
> hide #!9.3 models
> show #!9.3 models
> hide #!9.3 models
> show #!9.1 models
> show #!9.3 models
> hide #!9 models
> show #!8.4 models
> show #!8.3 models
> show #!8.2 models
> show #!8.1 models
> hide #!8.4 models
> show #!9 models
> hide #!9.1 models
> hide #!9.2 models
> hide #!9.3 models
> hide #!9.4 models
> show #!9.4 models
> show #!8.4 models
> hide #!8.4 models
> show #!8.4 models
> hide #!8.3 models
> show #!8.3 models
> hide #!8.1 models
> show #!8.1 models
> show #!3 models
> hide #!8 models
> hide #!9 models
> hide #!9.4 models
> show #!1 models
> hide #!1 models
> show #!8 models
> hide #!3 models
> hide #!8.1 models
> show #!8.1 models
> show #!9 models
> hide #!8 models
> show #!9.1 models
> show #!9.2 models
> show #!9.3 models
> show #!9.4 models
> hide #!9.3 models
> show #!9.3 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!9 models
> show #!9 models
> color zone #9.3 near #6 distance 15.53
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9.2 models
> show #!9.2 models
> hide #!9.2 models
> show #!9.2 models
> show #!7 models
> hide #!6 models
> hide #!9.2 models
> show #!9.2 models
> hide #!9.2 models
> show #!9.2 models
> color zone #9.3 near #6 distance 3.53
> color zone #9.3 near #6 distance 30.53
> color zone #9.3 near #6 distance 300.53
> color zone #9.3 near #6 distance 30.53
> color zone #9.3 near #6 distance 3.53
> color zone #9.3 near #6 distance 15.53
> volume splitbyzone #9.3
Opened coldshock_noncanonHiber_filt.mrc 2 0 as #2.1, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 2 1 as #2.2, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 2 2 as #2.3, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 2 3 as #2.4, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 2 4 as #2.5, grid size 232,232,232,
pixel 2.59, shown at level 0.00374, step 1, values float32
> show #!9.3 models
> hide #!9.3 models
> show #!9.3 models
> hide #!2 models
> hide #!9.1 models
> hide #!7 models
> hide #!9.2 models
> show #!8 models
> hide #!8.1 models
> hide #!8.3 models
> hide #!8.4 models
> hide #!8.5 models
> hide #!9.3 models
> show #!9.3 models
> hide #!8.2 models
> show #!8.2 models
> volume all level 0.0038
> show #!9.2 models
> hide #!9.2 models
> show #!9.2 models
> hide #!9.2 models
> show #!9.2 models
> hide #!9 models
> hide #!8 models
> show #!3 models
> color zone #3 near #6 distance 15.53
> volume splitbyzone #3
Opened coldshock_noncanonHiber_filt.mrc 0 as #4.1, grid size 232,232,232,
pixel 2.59, shown at level 0.0038, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 1 as #4.2, grid size 232,232,232,
pixel 2.59, shown at level 0.0038, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 2 as #4.3, grid size 232,232,232,
pixel 2.59, shown at level 0.0038, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 3 as #4.4, grid size 232,232,232,
pixel 2.59, shown at level 0.0038, step 1, values float32
Opened coldshock_noncanonHiber_filt.mrc 4 as #4.5, grid size 232,232,232,
pixel 2.59, shown at level 0.0038, step 1, values float32
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> ui tool show "Side View"
> view name sideview_noncanonical_1
> transparency #2.2 60
> transparency #4.2 60
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: MXCV3D/A
Chip: Apple M3
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: 90 Tage, 1 Stunde und 50 Minuten
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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
Installed Packages:
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.5.0
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
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: 1.2.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
pandas: 2.2.3
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pyarrow: 18.1.0
pycollada: 0.8
pydantic: 2.10.5
pydantic_core: 2.27.2
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.5.11
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
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 |
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