![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 weeks ago
Closed 2 weeks ago
#19740 closed defect (can't reproduce)
Crash drawing widget while processing QGraphicsScene event
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.7.3-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x0000000338497000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000033748b000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000033647f000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000335473000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000334467000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000033345b000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000033244f000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000331443000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000330437000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000032f42b000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000032e41f000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000032d413000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000032c407000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x00000002066e2240 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, PIL._imaging, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 56)
{"app_name":"ChimeraX","timestamp":"2026-01-16 15:57:35.00 -0500","app_version":"1.11.0","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.7.3 (24G419)","roots_installed":0,"name":"ChimeraX","incident_id":"8B3ABD66-06B2-48ED-846B-D719D4935252"}
{
"uptime" : 94000,
"procRole" : "Background",
"version" : 2,
"userID" : 747656469,
"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 106982,
"osVersion" : {
"train" : "macOS 15.7.3",
"build" : "24G419",
"releaseType" : "User"
},
"captureTime" : "2026-01-16 15:57:27.9096 -0500",
"codeSigningMonitor" : 1,
"incident" : "8B3ABD66-06B2-48ED-846B-D719D4935252",
"pid" : 82502,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-01-16 15:54:14.3102 -0500",
"procStartAbsTime" : 2275267722936,
"procExitAbsTime" : 2279913835998,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.0","CFBundleVersion":"1.11.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"325F5376-765E-5D90-89B5-358BBF350297","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E4BFA647-40CA-C641-3342-5652D24DFBEA",
"appleIntelligenceStatus" : {"reasons":["assetIsNotReady","notOptedIn","siriAssetIsNotReady"],"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" : "F0DC26A9-09FD-4BFA-820F-AF1109254FD6",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":82502},
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{
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Activity Tracing 256K 1
CG image 192K 10
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CoreAnimation 832K 52
CoreGraphics 48K 3
CoreUI image data 2944K 19
Foundation 16K 1
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__TPRO_CONST 128K 2
dyld private memory 1584K 15
mapped file 278.3M 55
page table in kernel 5895K 1
shared memory 3712K 27
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TOTAL, minus reserved VM space 13.2G 6150
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===== Log before crash start =====
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zhangj14/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/081125_yeast_ribosomes_WT_P51_v3_zoom_S12.cxs"
Opened cryosparc_P51_J40_map_sharp.mrc as #5, grid size 700,700,700, pixel
0.93, shown at level 0.0457, step 1, values float32
Opened cryosparc_P51_J67_003_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 0.93, shown at level 0.478, step 2, values float32
Log from Mon Aug 11 01:17:32 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/zhangj14/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v2.cxs"
Opened cryosparc_P51_J40_map_sharp.mrc as #5, grid size 700,700,700, pixel
0.93, shown at level 0.0968, step 1, values float32
Log from Sun Aug 10 00:06:22 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/zhangj14/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v2.cxs"
Opened cryosparc_P51_J28_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 1.55, shown at level 1.28, step 1, values float32
Opened cryosparc_P51_J30_004_volume_map_sharp.mrc as #3, grid size
300,300,300, pixel 1.55, shown at level 0.769, step 1, values float32
Opened cryosparc_P51_J40_map_sharp.mrc as #5, grid size 700,700,700, pixel
0.93, shown at level 0.0935, step 1, values float32
Log from Fri Aug 8 16:22:56 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/zhangj14 (Deleted)/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v1.cxs"
Opened cryosparc_P51_J28_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 1.55, shown at level 1.28, step 1, values float32
Opened cryosparc_P51_J30_004_volume_map_sharp.mrc as #3, grid size
300,300,300, pixel 1.55, shown at level 0.769, step 1, values float32
Log from Thu Aug 7 18:58:25 2025 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/zhangj14
> (Deleted)/Downloads/cryosparc_P51_J28_003_volume_map_sharp.mrc"
Opened cryosparc_P51_J28_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 1.55, shown at level 0.793, step 2, values float32
> volume #1 step 1
> volume #1 level 1.576
> volume #1 level 1.523
> ui tool show "Side View"
> open "/Users/zhangj14 (Deleted)/Downloads/7top.cif"
7top.cif title:
Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein
PR20 [more info...]
Chain information for 7top.cif #2
---
Chain | Description | UniProt
A25S | 25S rRNA |
A58S | 5.8S rRNA |
A5S | 5S rRNA |
AL02 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
AL03 | RPL3 isoform 1 | A0A6A5Q627_YEASX 1-387
AL04 | RPL4A isoform 1 | A0A6A5Q3W0_YEASX 1-362
AL05 | RPL5 isoform 1 | A0A6A5Q0W8_YEASX 1-297
AL06 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
AL07 | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
AL08 | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
AL09 | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
AL10 | RPL10 isoform 1 | A0A6A5PUZ5_YEASX 1-221
AL11 | RPL11A isoform 1 | A0A6A5Q7I9_YEASX 1-174
AL12 | Ribosomal protein L12 |
AL13 | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
AL14 | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
AL15 | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
AL16 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
AL17 | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
AL18 | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
AL19 | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
AL20 | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
AL21 | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
AL22 | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
AL23 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
AL24 | RPL24A isoform 1 | A0A6A5PY83_YEASX 1-155
AL25 | 60S ribosomal protein L25 | RL25_YEAST 1-142
AL26 | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
AL27 | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
AL28 | 60S ribosomal protein L28 | RL28_YEAST 1-149
AL29 | RPL29 isoform 1 | A0A6A5PWR1_YEASX 1-59
AL30 | 60S ribosomal protein L30 | RL30_YEAST 1-105
AL31 | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
AL32 | RPL32 isoform 1 | A0A6A5Q1M9_YEASX 1-130
AL33 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
AL34 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
AL35 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
AL36 | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
AL37 | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
AL38 | RPL38 isoform 1 | A0A6A5PUL8_YEASX 1-78
AL39 | 60S ribosomal protein L39 | RL39_YEAST 1-51
AL40 | Ubiquitin-60S ribosomal protein L40 | RL40A_YEAST 1-128
AL41 | 60S ribosomal protein L41-A | RL41A_YEAST 1-25
AL42 | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
AL43 | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ALP0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-198
APTN | tRNAfMet |
PR | PR20 | A7H9Z6_ANADF 5-44
Non-standard residues in 7top.cif #2
---
ZN — zinc ion
> show cartoons
> hide atoms
> select /AL03:226
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2
125433 atoms, 135363 bonds, 3255 pseudobonds, 9795 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,37.339,0,1,0,-7.8652,0,0,1,43.794
> view matrix models #2,1,0,0,15.226,0,1,0,28.613,0,0,1,32.277
> fitmap #2 inMap #1
Fit molecule 7top.cif (#2) to map cryosparc_P51_J28_003_volume_map_sharp.mrc
(#1) using 125433 atoms
average map value = 0.3492, steps = 144
shifted from previous position = 6.27
rotated from previous position = 8.68 degrees
atoms outside contour = 116214, contour level = 1.5227
Position of 7top.cif (#2) relative to
cryosparc_P51_J28_003_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99089020 0.13452979 -0.00619227 -13.88799278
-0.13378894 0.98860761 0.06896025 45.34920950
0.01539893 -0.06750357 0.99760019 49.26567799
Axis -0.45216577 -0.07154131 -0.88906015
Axis point 295.00396215 260.22396537 0.00000000
Rotation angle (degrees) 8.67909868
Shift along axis -40.76481803
> view matrix models
> #2,0.99089,0.13453,-0.0061923,-14.5,-0.13379,0.98861,0.06896,44.693,0.015399,-0.067504,0.9976,48.99
> view matrix models
> #2,0.99089,0.13453,-0.0061923,-104.83,-0.13379,0.98861,0.06896,-64.35,0.015399,-0.067504,0.9976,46.95
> volume #1 level 2.638
> volume #1 level 1.735
> view matrix models
> #2,0.99089,0.13453,-0.0061923,-146.61,-0.13379,0.98861,0.06896,-76.123,0.015399,-0.067504,0.9976,31.446
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.81638,0.57313,0.070995,-215.55,-0.33548,0.57071,-0.74949,209.85,-0.47008,0.58806,0.65819,62.897
> view matrix models
> #2,0.78972,0.61345,-0.005138,-203.53,-0.42589,0.5422,-0.72431,229.35,-0.44154,0.57419,0.68945,53.803
> view matrix models
> #2,0.53241,0.77534,-0.33969,-118.83,-0.68121,0.15423,-0.71565,359.47,-0.50249,0.61242,0.61029,73.874
> view
> view matrix models
> #2,0.017747,0.86222,-0.50622,1.3917,-0.91747,-0.1872,-0.35101,406.98,-0.39741,0.47067,0.78774,46.829
> view matrix models
> #2,0.89579,0.40774,0.17693,-218.59,-0.15365,0.6576,-0.73753,152.42,-0.41707,0.63349,0.65173,43.978
> view matrix models
> #2,0.92345,0.28201,0.2602,-214.72,-0.019791,0.71222,-0.70167,106.8,-0.3832,0.64281,0.66329,32.869
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.92345,0.28201,0.2602,-127.47,-0.019791,0.71222,-0.70167,238.57,-0.3832,0.64281,0.66329,55.488
> view matrix models
> #2,0.92345,0.28201,0.2602,-88.009,-0.019791,0.71222,-0.70167,210.27,-0.3832,0.64281,0.66329,33.026
> view matrix models
> #2,0.92345,0.28201,0.2602,-64.258,-0.019791,0.71222,-0.70167,222.79,-0.3832,0.64281,0.66329,42.61
> view matrix models
> #2,0.92345,0.28201,0.2602,-64.446,-0.019791,0.71222,-0.70167,217,-0.3832,0.64281,0.66329,38.565
> fitmap #2 inMap #1
Fit molecule 7top.cif (#2) to map cryosparc_P51_J28_003_volume_map_sharp.mrc
(#1) using 125433 atoms
average map value = 0.3626, steps = 144
shifted from previous position = 14.3
rotated from previous position = 5.75 degrees
atoms outside contour = 119148, contour level = 1.7351
Position of 7top.cif (#2) relative to
cryosparc_P51_J28_003_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.94187225 0.29405715 0.16250249 -63.44801747
-0.08985543 0.68653751 -0.72152079 242.63156198
-0.32373240 0.66497868 0.67305326 27.00875393
Axis 0.91300212 0.32018295 -0.25280428
Axis point 0.00000000 96.39338650 288.66217751
Rotation angle (degrees) 49.40322263
Shift along axis 12.93038697
> hide #!2 models
> volume #1 color #0096ff
> volume #1 color #0096ff83
> volume #1 level 1.284
> open "/Users/zhangj14
> (Deleted)/Downloads/cryosparc_P51_J30_004_volume_map_sharp.mrc"
Opened cryosparc_P51_J30_004_volume_map_sharp.mrc as #3, grid size
300,300,300, pixel 1.55, shown at level 0.921, step 2, values float32
> volume #3 step 1
> select #3
3 models selected
> view matrix models #3,1,0,0,41.414,0,1,0,174.22,0,0,1,47.926
Drag select of 3 cryosparc_P51_J30_004_volume_map_sharp.mrc
> view matrix models #3,1,0,0,42.712,0,1,0,65.405,0,0,1,-33.01
> volume #3 level 1.009
> select clear
> volume #3 level 0.9648
> volume #3 level 0.9298
> volume #3 color #0433ff
> volume #3 color #0433ff7c
> volume #3 color #0433ff7d
> set bgColor white
> save "/Users/zhangj14 (Deleted)/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v1.cxs"
> includeMaps true
> show #!2 models
> select /A25S:1734
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #2
125433 atoms, 135363 bonds, 3255 pseudobonds, 9795 residues, 4 models selected
> select subtract #2
Nothing selected
> select add #2
125433 atoms, 135363 bonds, 3255 pseudobonds, 9795 residues, 4 models selected
> view matrix models
> #2,0.94187,0.29406,0.1625,-48.381,-0.089855,0.68654,-0.72152,324.99,-0.32373,0.66498,0.67305,7.466
> view matrix models
> #2,0.94187,0.29406,0.1625,-16.075,-0.089855,0.68654,-0.72152,206.16,-0.32373,0.66498,0.67305,126.84
> view matrix models
> #2,0.94187,0.29406,0.1625,-16.044,-0.089855,0.68654,-0.72152,155,-0.32373,0.66498,0.67305,56.359
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.15743,-0.65047,-0.74304,578.88,-0.30321,-0.68424,0.66324,210.21,-0.93983,0.32971,-0.089511,399.63
> view matrix models
> #2,0.7385,-0.67337,-0.034472,261.96,-0.19338,-0.26051,0.94591,46.014,-0.64593,-0.69188,-0.3226,593.66
> open 8CCS
Summary of feedback from opening 8CCS fetched from pdb
---
notes | Fetching compressed mmCIF 8ccs from http://files.rcsb.org/download/8ccs.cif
Fetching CCD 1MA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/1MA/1MA.cif
Fetching CCD 4AC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/4AC/4AC.cif
Fetching CCD 5MC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/5MC/5MC.cif
Fetching CCD A2M from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/A2M/A2M.cif
Fetching CCD B8N from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/B8N/B8N.cif
Fetching CCD G7M from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/G7M/G7M.cif
Fetching CCD MA6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/MA6/MA6.cif
Fetching CCD OMC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/OMC/OMC.cif
Fetching CCD OMG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/OMG/OMG.cif
Fetching CCD OMU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/OMU/OMU.cif
Fetching CCD SPD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/SPD/SPD.cif
Fetching CCD UR3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/UR3/UR3.cif
Fetching CCD YYG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/YYG/YYG.cif
8ccs title:
80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1)
complex [more info...]
Chain information for 8ccs #4
---
Chain | Description | UniProt
0 | 40S ribosomal protein S24-A | RS24A_YEAST 1-135
1 | 40S ribosomal protein S25-A | RS25A_YEAST 1-108
2 | 40S ribosomal protein S26 | A0A6A5PUG0_YEASX 1-119
3 | 40S ribosomal protein S27-A | RS27A_YEAST 1-82
4 | 40S ribosomal protein S28-A | RS28A_YEAST 1-67
5 | HLJ1_G0030400.mRNA.1.CDS.1 | A0A6A5PV92_YEASX 1-56
6 | 40S ribosomal protein S30-A | RS30A_YEAST 1-63
7 | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319
8 | Ubiquitin-40S ribosomal protein S31 | A0A6A5PU37_YEASX 1-152
A | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
AA | 25S ribosomal RNA |
B | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
BB | 5S ribosomal RNA |
Bb | Transfer RNA Phe |
C | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
CC | 5.8S ribosomal RNA |
Cc | Transfer RNA fMet |
D | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
DD | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312
Dd | Messenger RNA |
E | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
EE | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Ee | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
F | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
FF | 60S ribosomal protein L3 | RL3_YEAST 1-387
G | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
GG | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
H | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
HH | 60S ribosomal protein L5 | RL5_YEAST 1-297
I | 60S ribosomal protein L24-A | RL24A_YEAST 1-155
II | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
J | 60S ribosomal protein L25 | RL25_YEAST 1-142
JJ | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
K | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
KK | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
L | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
LL | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
M | 60S ribosomal protein L28 | RL28_YEAST 1-149
MM | 60S ribosomal protein L10 | RL10_YEAST 1-221
N | 60S ribosomal protein L29 | RL29_YEAST 1-59
NN | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
O | 60S ribosomal protein L30 | RL30_YEAST 1-105
OO | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
P | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
PP | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
Pp | di-peptide |
Q | 60S ribosomal protein L32 | RL32_YEAST 1-130
QQ | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
R | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
S | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
T | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
U | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
V | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
W | 60S ribosomal protein L38 | RL38_YEAST 1-78
X | 60S ribosomal protein L39 | RL39_YEAST 1-51
Y | Ubiquitin-60S ribosomal protein L40 | RL40A_YEAST 1-128
Z | 60S ribosomal protein L41-A | RL41A_YEAST 1-25
a | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
b | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
c | 18S ribosomal RNA |
d | 40S ribosomal protein S0-A | RSSA1_YEAST 1-252
e | 40S ribosomal protein S1-A | RS3A1_YEAS7 1-255
f | 40S ribosomal protein S2 | RS2_YEAST 1-254
g | RPS3 isoform 1 | A0A6A5Q3Q1_YEASX 1-240
h | 40S ribosomal protein S4-A | RS4A_YEAST 1-261
i | 40S ribosomal protein S5 | RS5_YEAST 1-225
j | 40S ribosomal protein S6-A | RS6A_YEAST 1-236
k | 40S ribosomal protein S7-A | RS7A_YEAST 1-190
l | 40S ribosomal protein S8-B | RS8B_YEAST 1-200
m | 40S ribosomal protein S9-A | RS9A_YEAST 1-197
n | 40S ribosomal protein S10-A | RS10A_YEAST 1-105
o | 40S ribosomal protein S11-A | RS11A_YEAST 1-156
p | 40S ribosomal protein S13 | RS13_YEAST 1-151
q | 40S ribosomal protein S14-A | RS14A_YEAST 1-137
r | 40S ribosomal protein S15 | RS15_YEAST 1-142
s | 40S ribosomal protein S16-A | RS16A_YEAST 1-143
t | 40S ribosomal protein S17-A | RS17A_YEAST 1-136
u | 40S ribosomal protein S18-A | RS18A_YEAST 1-146
v | 40S ribosomal protein S19-A | RS19A_YEAST 1-144
w | 40S ribosomal protein S20 | A0A6A5PVE9_YEASX 1-121
x | 40S ribosomal protein S21-A | RS21A_YEAST 1-87
y | 40S ribosomal protein S22-A | RS22A_YEAST 1-130
z | 40S ribosomal protein S23-A | RS23A_YEAST 1-145
Non-standard residues in 8ccs #4
---
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
K — potassium ion
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> hide sel atoms
> show sel cartoons
> hide #!2 models
> select subtract #2
Nothing selected
> hide #!4 models
> show #!4 models
> nucleotides #!4 atoms
> style nucleic & #!4 stick
Changed 112013 atom styles
> hide #!4 atoms
> show #!4 cartoons
> select #4/AA:978
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #4
201697 atoms, 215006 bonds, 6540 pseudobonds, 17908 residues, 4 models
selected
> view matrix models
> #4,-0.30464,0.5358,-0.78747,419.87,-0.92389,0.03476,0.38107,410.09,0.23155,0.84363,0.48443,-153.24
> view matrix models
> #4,0.85587,0.51644,-0.027796,-94.582,-0.47758,0.8098,0.3408,88.636,0.19851,-0.2784,0.93973,38.738
> view matrix models
> #4,0.08915,0.71993,-0.68829,236.22,-0.96445,0.23499,0.12088,436.92,0.24877,0.65305,0.71529,-168.44
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.08915,0.71993,-0.68829,295.31,-0.96445,0.23499,0.12088,304.27,0.24877,0.65305,0.71529,-25.517
> view matrix models
> #4,0.08915,0.71993,-0.68829,306.56,-0.96445,0.23499,0.12088,289.54,0.24877,0.65305,0.71529,-5.9918
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.65825,-0.75262,0.016467,363.86,0.7524,0.65846,0.018203,-262.41,-0.024543,0.00040782,0.9997,169.05
> view matrix models
> #4,0.0082103,-0.91944,-0.39315,696.24,0.8551,0.21028,-0.4739,-34.279,0.51839,-0.3323,0.78794,170.6
> view matrix models
> #4,0.49911,-0.84609,-0.18716,487.63,0.85242,0.51822,-0.069464,-227.36,0.15576,-0.12487,0.97987,159.91
> view matrix models
> #4,0.78277,-0.62183,0.024392,292.32,0.62229,0.78242,-0.023882,-249.69,-0.0042348,0.033873,0.99942,154.49
> view matrix models
> #4,0.84679,0.43289,-0.30911,77.328,-0.45595,0.29142,-0.84094,397.51,-0.27395,0.85304,0.44415,154.21
> view matrix models
> #4,0.5428,0.70459,-0.45707,125.41,-0.83478,0.39284,-0.38578,348.77,-0.092263,0.59095,0.80141,79.805
> view matrix models
> #4,0.39742,0.78381,-0.47718,148.52,-0.90105,0.23491,-0.36459,404.08,-0.17368,0.57486,0.79961,106.7
> view matrix models
> #4,0.53496,0.76611,-0.35623,83.375,-0.84447,0.4717,-0.25371,294.03,-0.026333,0.43655,0.89929,77.616
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.53496,0.76611,-0.35623,-0.25029,-0.84447,0.4717,-0.25371,455.1,-0.026333,0.43655,0.89929,-164.88
> view matrix models
> #4,0.53496,0.76611,-0.35623,7.6398,-0.84447,0.4717,-0.25371,460.32,-0.026333,0.43655,0.89929,-161.22
> view matrix models
> #4,0.53496,0.76611,-0.35623,7.065,-0.84447,0.4717,-0.25371,472.76,-0.026333,0.43655,0.89929,-163.65
> view matrix models
> #4,0.53496,0.76611,-0.35623,6.1842,-0.84447,0.4717,-0.25371,471.71,-0.026333,0.43655,0.89929,-160.45
> fitmap #4 inMap #3
Fit molecule 8ccs (#4) to map cryosparc_P51_J30_004_volume_map_sharp.mrc (#3)
using 201697 atoms
average map value = 0.3242, steps = 140
shifted from previous position = 13.2
rotated from previous position = 9.4 degrees
atoms outside contour = 174799, contour level = 0.92983
Position of 8ccs (#4) relative to cryosparc_P51_J30_004_volume_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
0.61327937 0.75684858 -0.22598371 -80.64572258
-0.77773143 0.52865799 -0.34008022 390.79789583
-0.13792114 0.38431882 0.91283997 -79.64002910
Axis 0.42630559 -0.05182443 -0.90309345
Axis point 330.73846119 285.28803133 0.00000000
Rotation angle (degrees) 58.17081343
Shift along axis 17.28978881
> view matrix models
> #4,0.61328,0.75685,-0.22598,86.167,-0.77773,0.52866,-0.34008,276.32,-0.13792,0.38432,0.91284,-143.95
> view matrix models
> #4,0.61328,0.75685,-0.22598,86.863,-0.77773,0.52866,-0.34008,241.08,-0.13792,0.38432,0.91284,-119.51
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.78661,-0.60007,-0.14547,388.86,0.61703,0.77261,0.1495,-335.37,0.022682,-0.20736,0.978,-18.966
> view matrix models
> #4,-0.93576,-0.16159,0.31343,610.22,-0.072479,0.95799,0.2775,-234.34,-0.3451,0.23696,-0.90816,470.6
> view matrix models
> #4,-0.39924,-0.87006,0.28914,665.31,-0.91613,0.36607,-0.16341,275,0.036338,-0.33013,-0.94324,531.92
> view matrix models
> #4,-0.046058,-0.99795,0.044359,671.16,-0.77851,0.0080341,-0.62758,461.49,0.62594,-0.063439,-0.77729,254.68
> view matrix models
> #4,-0.67415,-0.68926,-0.2654,840.63,-0.59799,0.72027,-0.35159,143.27,0.4335,-0.078318,-0.89775,343.43
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.67415,-0.68926,-0.2654,701.6,-0.59799,0.72027,-0.35159,352.46,0.4335,-0.078318,-0.89775,332.61
> view matrix models
> #4,-0.67415,-0.68926,-0.2654,704.41,-0.59799,0.72027,-0.35159,341.63,0.4335,-0.078318,-0.89775,344.13
> view matrix models
> #4,-0.67415,-0.68926,-0.2654,720.57,-0.59799,0.72027,-0.35159,346.87,0.4335,-0.078318,-0.89775,338.99
> view matrix models
> #4,-0.67415,-0.68926,-0.2654,716.3,-0.59799,0.72027,-0.35159,354.68,0.4335,-0.078318,-0.89775,341.07
> fitmap #4 inMap #3
Fit molecule 8ccs (#4) to map cryosparc_P51_J30_004_volume_map_sharp.mrc (#3)
using 201697 atoms
average map value = 0.7965, steps = 340
shifted from previous position = 9.96
rotated from previous position = 36.3 degrees
atoms outside contour = 125413, contour level = 0.92983
Position of 8ccs (#4) relative to cryosparc_P51_J30_004_volume_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
-0.94386421 -0.31230302 0.10764374 539.62589137
-0.32537200 0.93520865 -0.13970629 106.53858828
-0.05703866 -0.16688803 -0.98432463 560.71405021
Axis -0.16235518 0.98363986 -0.07806040
Axis point 290.51169275 0.00000000 273.17526891
Rotation angle (degrees) 175.19810990
Shift along axis -26.58501715
> select clear
> volume #3 level 0.7986
> hide #!4 models
> show #!4 models
> save "/Users/zhangj14 (Deleted)/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v1.cxs"
> includeMaps true
> save "/Users/zhangj14 (Deleted)/Desktop/image1.png" supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode "/Users/zhangj14 (Deleted)/Desktop/movie1.mp4"
Movie saved to /Users/zhangj14 (Deleted)/Desktop/movie1.mp4
> volume #3 level 0.8861
> show #!4 atoms
> style #!4 stick
Changed 201697 atom styles
> volume #3 level 0.6626
> volume #3 level 0.769
> save "/Users/zhangj14 (Deleted)/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v1.cxs"
> includeMaps true
——— End of log from Thu Aug 7 18:58:25 2025 ———
opened ChimeraX session
> open "/Users/zhangj14 (Deleted)/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/cryosparc_P51_J40_map_sharp.mrc"
Opened cryosparc_P51_J40_map_sharp.mrc as #5, grid size 700,700,700, pixel
0.93, shown at step 1, values float32
> volume #5 level -9.265e-06,0 level 0.1272,0.8 level 1.726,1
> volume #5 region 0,0,0,699,699,699 step 4
[Repeated 1 time(s)]
> volume #5 level 0.0722
> volume #5 color #ff40ff
> volume #5 color #ff40ff82
> volume #5 step 2
Drag select of 5 cryosparc_P51_J40_map_sharp.mrc
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-91.967,0,1,0,196.26,0,0,1,-182.27
> view matrix models #5,1,0,0,-73.35,0,1,0,199.08,0,0,1,-198.02
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-46.563,0,1,0,-33.52,0,0,1,-114.05
> select add #5
5 models selected
> select add #5
5 models selected
> select add #5
5 models selected
> select add #5
5 models selected
> hide #!4 models
> fitmap #5 inMap #3
Fit map cryosparc_P51_J40_map_sharp.mrc in map
cryosparc_P51_J30_004_volume_map_sharp.mrc using 169901 points
correlation = 0.8787, correlation about mean = 0.6972, overlap = 7.071e+04
steps = 156, shift = 7.13, angle = 16.4 degrees
Position of cryosparc_P51_J40_map_sharp.mrc (#5) relative to
cryosparc_P51_J30_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.96857314 -0.24261307 -0.05481755 10.60702797
0.24785332 0.95990789 0.13094114 -202.04971599
0.02085177 -0.14041278 0.98987345 -43.31356925
Axis -0.47975340 -0.13378326 0.86714400
Axis point 808.75885917 -91.92424921 0.00000000
Rotation angle (degrees) 16.42772453
Shift along axis -15.61698922
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #5 color #0096ff
> volume #5 color #76d6ff
> volume #5 color #7a81ff
> volume #5 step 1
> volume #5 level 0.119
> select clear
> show #!4 models
> volume #5 color #7a81ff7d
Drag select of 250 atoms, 63 residues, 12 pseudobonds, 232 bonds, 5
cryosparc_P51_J40_map_sharp.mrc
> select clear
> ui tool show "Side View"
> hide #!4 atoms
Drag select of 111 residues, 5 cryosparc_P51_J40_map_sharp.mrc
> select clear
> volume #5 level 0.09347
> save "/Users/zhangj14 (Deleted)/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v2.cxs"
> includeMaps true
——— End of log from Fri Aug 8 16:22:56 2025 ———
opened ChimeraX session
> view
> ui tool show "Side View"
> volume #5 level 0.3563
> close #3
> close #1
> volume #5 level 0.1946
> color #4 #942193ff
> hide #!4 cartoons
> show #!4 atoms
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> style #!4 ball
Changed 201697 atom styles
> color #!4 byhetero
> rainbow #!4
> color #!4 byhetero
> nucleotides #!4 atoms
> style nucleic & #!4 stick
Changed 112013 atom styles
> show #!4 cartoons
> hide #!4 atoms
> nucleotides #!4 atoms
> style nucleic & #!4 stick
Changed 112013 atom styles
> nucleotides #!4 atoms
> style nucleic & #!4 stick
Changed 112013 atom styles
> nucleotides #!4 atoms
> style nucleic & #!4 stick
Changed 112013 atom styles
> nucleotides #!4 fill
> style nucleic & #!4 stick
Changed 112013 atom styles
> nucleotides #!4 fill
> style nucleic & #!4 stick
Changed 112013 atom styles
> nucleotides #!4 ladder
> nucleotides #!4 stubs
> select add #4
201697 atoms, 215006 bonds, 6540 pseudobonds, 17908 residues, 4 models
selected
> nucleotides sel stubs
> nucleotides sel atoms
> style nucleic & sel stick
Changed 112013 atom styles
> show sel atoms
> style sel stick
Changed 201697 atom styles
> hide sel atoms
> save "/Users/zhangj14/Google Drive/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v2.cxs"
> volume #5 level 0.1564
> volume #5 level 0.09679
> volume #5 color darkgrey
> volume #5 color #a9a9a976
> volume #5 color #a9a9a975
> volume #5 color #797979
> volume #5 color #79797976
> volume #5 color #ebebeb
> volume #5 color #ebebeb83
> show sel atoms
> hide sel atoms
> lighting simple
> lighting full
> save "/Users/zhangj14/Google Drive/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v2.cxs"
——— End of log from Sun Aug 10 00:06:22 2025 ———
opened ChimeraX session
> open "/Users/zhangj14/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/cryosparc_P51_J67_003_volume_map_sharp.mrc"
Opened cryosparc_P51_J67_003_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 0.93, shown at level 0.357, step 2, values float32
> volume #1 level 0.5205
> select subtract #4
Nothing selected
> hide #!4 models
> hide #!1 models
> show #!1 models
> color #1 #008f00ff models
> color #1 #008f0087 models
> select #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,44.72,0,1,0,-2.3368,0,0,1,-230.93
> view matrix models #1,1,0,0,51.117,0,1,0,-21.257,0,0,1,-218.17
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.12973,0.99149,0.011016,1.0388,-0.85062,0.10557,0.51506,302.26,0.50952,-0.076189,0.85708,-289.64
> view matrix models
> #1,0.014963,-0.07744,-0.99688,524.05,-0.20749,-0.97554,0.072667,523.74,-0.97812,0.20575,-0.030664,187.2
> view matrix models
> #1,0.33833,0.91583,-0.21629,19.95,-0.065775,-0.20626,-0.97628,518.66,-0.93873,0.34453,-0.0095464,137.26
> view matrix models
> #1,-0.60235,0.6319,-0.48773,378.04,0.023864,-0.59649,-0.80227,560.29,-0.79788,-0.49488,0.34421,243.74
> view matrix models
> #1,-0.71226,0.57949,-0.39609,398.06,-0.22009,-0.72021,-0.65792,619.45,-0.66652,-0.38144,0.64051,118.5
> view matrix models
> #1,-0.51225,0.23374,-0.82642,533.01,-0.039985,-0.9677,-0.24891,551.39,-0.85791,-0.094459,0.50505,119.62
> view matrix models
> #1,-0.37195,0.13187,0.91884,146.5,-0.91248,0.12978,-0.388,507.05,-0.17041,-0.98274,0.072056,278.53
> hide #!1 models
> select subtract #1
Nothing selected
> show #!4 models
> volume #1 level 0.4781
> volume #5 level 0.08828
> volume #5 level 0.07552
> split #4
Split 8ccs (#4) into 83 models
Chain information for 8ccs 0 #4.1
---
Chain | Description
0 | No description available
Chain information for 8ccs 1 #4.2
---
Chain | Description
1 | No description available
Chain information for 8ccs 2 #4.3
---
Chain | Description
2 | No description available
Chain information for 8ccs 3 #4.4
---
Chain | Description
3 | No description available
Chain information for 8ccs 4 #4.5
---
Chain | Description
4 | No description available
Chain information for 8ccs 5 #4.6
---
Chain | Description
5 | No description available
Chain information for 8ccs 6 #4.7
---
Chain | Description
6 | No description available
Chain information for 8ccs 7 #4.8
---
Chain | Description
7 | No description available
Chain information for 8ccs 8 #4.9
---
Chain | Description
8 | No description available
Chain information for 8ccs A #4.10
---
Chain | Description
A | No description available
Chain information for 8ccs AA #4.11
---
Chain | Description
AA | No description available
Chain information for 8ccs B #4.12
---
Chain | Description
B | No description available
Chain information for 8ccs BB #4.13
---
Chain | Description
BB | No description available
Chain information for 8ccs Bb #4.14
---
Chain | Description
Bb | No description available
Chain information for 8ccs C #4.15
---
Chain | Description
C | No description available
Chain information for 8ccs CC #4.16
---
Chain | Description
CC | No description available
Chain information for 8ccs Cc #4.17
---
Chain | Description
Cc | No description available
Chain information for 8ccs D #4.18
---
Chain | Description
D | No description available
Chain information for 8ccs DD #4.19
---
Chain | Description
DD | No description available
Chain information for 8ccs Dd #4.20
---
Chain | Description
Dd | No description available
Chain information for 8ccs E #4.21
---
Chain | Description
E | No description available
Chain information for 8ccs EE #4.22
---
Chain | Description
EE | No description available
Chain information for 8ccs Ee #4.23
---
Chain | Description
Ee | No description available
Chain information for 8ccs F #4.24
---
Chain | Description
F | No description available
Chain information for 8ccs FF #4.25
---
Chain | Description
FF | No description available
Chain information for 8ccs G #4.26
---
Chain | Description
G | No description available
Chain information for 8ccs GG #4.27
---
Chain | Description
GG | No description available
Chain information for 8ccs H #4.28
---
Chain | Description
H | No description available
Chain information for 8ccs HH #4.29
---
Chain | Description
HH | No description available
Chain information for 8ccs I #4.30
---
Chain | Description
I | No description available
Chain information for 8ccs II #4.31
---
Chain | Description
II | No description available
Chain information for 8ccs J #4.32
---
Chain | Description
J | No description available
Chain information for 8ccs JJ #4.33
---
Chain | Description
JJ | No description available
Chain information for 8ccs K #4.34
---
Chain | Description
K | No description available
Chain information for 8ccs KK #4.35
---
Chain | Description
KK | No description available
Chain information for 8ccs L #4.36
---
Chain | Description
L | No description available
Chain information for 8ccs LL #4.37
---
Chain | Description
LL | No description available
Chain information for 8ccs M #4.38
---
Chain | Description
M | No description available
Chain information for 8ccs MM #4.39
---
Chain | Description
MM | No description available
Chain information for 8ccs N #4.40
---
Chain | Description
N | No description available
Chain information for 8ccs NN #4.41
---
Chain | Description
NN | No description available
Chain information for 8ccs O #4.42
---
Chain | Description
O | No description available
Chain information for 8ccs OO #4.43
---
Chain | Description
OO | No description available
Chain information for 8ccs P #4.44
---
Chain | Description
P | No description available
Chain information for 8ccs PP #4.45
---
Chain | Description
PP | No description available
Chain information for 8ccs Pp #4.46
---
Chain | Description
Pp | No description available
Chain information for 8ccs Q #4.47
---
Chain | Description
Q | No description available
Chain information for 8ccs QQ #4.48
---
Chain | Description
QQ | No description available
Chain information for 8ccs R #4.49
---
Chain | Description
R | No description available
Chain information for 8ccs S #4.50
---
Chain | Description
S | No description available
Chain information for 8ccs T #4.51
---
Chain | Description
T | No description available
Chain information for 8ccs U #4.52
---
Chain | Description
U | No description available
Chain information for 8ccs V #4.53
---
Chain | Description
V | No description available
Chain information for 8ccs W #4.54
---
Chain | Description
W | No description available
Chain information for 8ccs X #4.55
---
Chain | Description
X | No description available
Chain information for 8ccs Y #4.56
---
Chain | Description
Y | No description available
Chain information for 8ccs Z #4.57
---
Chain | Description
Z | No description available
Chain information for 8ccs a #4.58
---
Chain | Description
a | No description available
Chain information for 8ccs b #4.59
---
Chain | Description
b | No description available
Chain information for 8ccs c #4.60
---
Chain | Description
c | No description available
Chain information for 8ccs d #4.61
---
Chain | Description
d | No description available
Chain information for 8ccs e #4.62
---
Chain | Description
e | No description available
Chain information for 8ccs f #4.63
---
Chain | Description
f | No description available
Chain information for 8ccs g #4.64
---
Chain | Description
g | No description available
Chain information for 8ccs h #4.65
---
Chain | Description
h | No description available
Chain information for 8ccs i #4.66
---
Chain | Description
i | No description available
Chain information for 8ccs j #4.67
---
Chain | Description
j | No description available
Chain information for 8ccs k #4.68
---
Chain | Description
k | No description available
Chain information for 8ccs l #4.69
---
Chain | Description
l | No description available
Chain information for 8ccs m #4.70
---
Chain | Description
m | No description available
Chain information for 8ccs n #4.71
---
Chain | Description
n | No description available
Chain information for 8ccs o #4.72
---
Chain | Description
o | No description available
Chain information for 8ccs p #4.73
---
Chain | Description
p | No description available
Chain information for 8ccs q #4.74
---
Chain | Description
q | No description available
Chain information for 8ccs r #4.75
---
Chain | Description
r | No description available
Chain information for 8ccs s #4.76
---
Chain | Description
s | No description available
Chain information for 8ccs t #4.77
---
Chain | Description
t | No description available
Chain information for 8ccs u #4.78
---
Chain | Description
u | No description available
Chain information for 8ccs v #4.79
---
Chain | Description
v | No description available
Chain information for 8ccs w #4.80
---
Chain | Description
w | No description available
Chain information for 8ccs x #4.81
---
Chain | Description
x | No description available
Chain information for 8ccs y #4.82
---
Chain | Description
y | No description available
Chain information for 8ccs z #4.83
---
Chain | Description
z | No description available
> select add #4.83
1122 atoms, 1139 bonds, 145 residues, 1 model selected
> select subtract #4.83
Nothing selected
> select add #4.83
1122 atoms, 1139 bonds, 145 residues, 1 model selected
> volume #5 level 0.1138
> volume #5 color #ebebebb6
> volume #5 color #ebebebda
> volume #5 color #011993
> volume #5 color #011993cc
> volume #5 color #011993b1
> volume #5 color #011993b0
> volume #5 level 0.08403
> view sel
> ui tool show "Side View"
> lighting shadows false
> hide #4.83 models
> show #4.83 models
> hide #4.83 models
> show #4.83 models
> hide #!4 models
> select subtract #4.83
Nothing selected
> select add #4.83
1122 atoms, 1139 bonds, 145 residues, 1 model selected
> show #!4 models
> hide #4.1 models
> hide #4.2 models
> hide #!4.3 models
> hide #4.4 models
> hide #4.5 models
> hide #!4.6 models
> hide #4.7 models
> hide #4.8 models
> hide #!4.9 models
> hide #4.10 models
> hide #!4.11 models
> hide #!4.12 models
> show #!4.11 models
> hide #!4.11 models
> hide #!4.13 models
> hide #!4.14 models
> show #!4.14 models
> hide #4.15 models
> hide #!4.16 models
> hide #!4.17 models
> hide #4.18 models
> show #!4.17 models
> hide #4.19 models
> hide #!4.20 models
> hide #4.21 models
> hide #!4.22 models
> hide #4.23 models
> hide #4.24 models
> hide #!4.25 models
> hide #4.26 models
> hide #4.27 models
> hide #!4.28 models
> hide #4.29 models
> hide #4.30 models
> hide #!4.31 models
> hide #4.32 models
> hide #4.33 models
> hide #4.34 models
> hide #4.35 models
> hide #4.36 models
> hide #4.37 models
> hide #4.38 models
> hide #!4.39 models
> hide #4.40 models
> show #4.38 models
> hide #4.38 models
> hide #4.41 models
> show #4.41 models
> hide #4.41 models
> hide #4.42 models
> hide #4.43 models
> hide #4.44 models
> hide #4.45 models
> hide #4.46 models
> hide #!4.47 models
> hide #!4.48 models
> hide #4.49 models
> hide #!4.50 models
> hide #4.51 models
> hide #4.52 models
> hide #!4.53 models
> hide #4.54 models
> hide #4.55 models
> hide #!4.56 models
> hide #4.57 models
> hide #!4.58 models
> hide #!4.59 models
> hide #!4.60 models
> show #!4.60 models
> hide #4.61 models
> hide #4.62 models
> hide #4.63 models
> hide #4.64 models
> hide #4.65 models
> hide #!4.66 models
> hide #4.67 models
> show #4.67 models
> hide #4.67 models
> hide #4.68 models
> hide #!4.69 models
> hide #4.70 models
> show #4.70 models
> hide #4.70 models
> hide #4.71 models
> hide #4.72 models
> hide #4.73 models
> hide #!4.74 models
> hide #!4.75 models
> hide #4.76 models
> hide #4.77 models
> hide #4.78 models
> show #4.78 models
> hide #4.78 models
> hide #4.79 models
> hide #4.80 models
> hide #4.81 models
> hide #4.82 models
> hide #4.83 models
> show #4.83 models
> hide #!5 models
> show #!5 models
> save "/Users/zhangj14/Google Drive/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/081125_yeast_ribosomes_WT_P51_v3_zoom_S12.cxs"
> includeMaps true
> color #4 #919191ff models
> color #4 #fffb00ff models
> color #4 #945200ff models
> color #4.83 #942193ff
> select subtract #4.83
Nothing selected
> volume #5 level 0.05425
> show #!4.20 models
> color #4.20 #00f900ff
> color #4.20 #00fdffff
> select add #4.17
1651 atoms, 1836 bonds, 82 pseudobonds, 84 residues, 3 models selected
> select subtract #4.17
Nothing selected
> select add #4.14
1644 atoms, 1831 bonds, 74 pseudobonds, 82 residues, 3 models selected
> color #4.14 #00f900ff
> select subtract #4.14
Nothing selected
> save "/Users/zhangj14/Google Drive/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/081125_yeast_ribosomes_WT_P51_v3_zoom_S12.cxs"
> includeMaps true
> volume #5 level 0.04574
> select add #4.20
283 atoms, 311 bonds, 2 pseudobonds, 18 residues, 2 models selected
> select subtract #4.20
Nothing selected
> select add #4.20
283 atoms, 311 bonds, 2 pseudobonds, 18 residues, 2 models selected
> show sel atoms
> select subtract #4.20
Nothing selected
> hide #!4.60 models
> show #!4.60 models
> color #4.60 #7a81ffff
> color #4.60 #5254ffff
> color #4.60 #81c4ffff
> color #4.60 #ff3a2cff
> color #4.60 #ff4486ff
> color #4.60 #fff61eff
> color #4.60 #4bff26ff
> color #4.60 #b31cffff
> color #4.60 #d627ffff
> color #4.60 #55fff5ff
> color #4.60 #26ff3dff
> color #4.60 #ff9517ff
> save "/Users/zhangj14/Google Drive/My Drive/Cryo-
> EM/2025_Ribosomes/080725_WT_Glacios/081125_yeast_ribosomes_WT_P51_v3_zoom_S12.cxs"
——— End of log from Mon Aug 11 01:17:32 2025 ———
> view name session-start
opened ChimeraX session
> volume #5 level 0.02447
> sequence chain #2/A25S
Alignment identifier is 2/A25S
> sequence chain #2/A58S#4.16/CC
Alignment identifier is 1
> sequence chain #2/A5S#4.13/BB
Alignment identifier is 2
> sequence chain #2/AL02
Alignment identifier is 2/AL02
> sequence chain #2/AL03
Alignment identifier is 2/AL03
> sequence chain #2/AL04
Alignment identifier is 2/AL04
> sequence chain #2/AL05
Alignment identifier is 2/AL05
> sequence chain #2/AL06
Alignment identifier is 2/AL06
> sequence chain #2/AL07
Alignment identifier is 2/AL07
> sequence chain #2/AL08
Alignment identifier is 2/AL08
> sequence chain #2/AL09#4.37/LL
Alignment identifier is 3
> sequence chain #2/AL10
Alignment identifier is 2/AL10
> sequence chain #2/AL11
Alignment identifier is 2/AL11
> sequence chain #2/AL12
Alignment identifier is 2/AL12
> sequence chain #2/AL13
Alignment identifier is 2/AL13
> sequence chain #2/AL14
Alignment identifier is 2/AL14
> sequence chain #2/AL15
Alignment identifier is 2/AL15
> sequence chain #2/AL16
Alignment identifier is 2/AL16
> sequence chain #2/AL17
Alignment identifier is 2/AL17
> sequence chain #2/AL18
Alignment identifier is 2/AL18
> sequence chain #2/AL19
Alignment identifier is 2/AL19
> sequence chain #2/AL20#4.21/E
Alignment identifier is 4
> sequence chain #2/AL21
Alignment identifier is 2/AL21
> sequence chain #2/AL22
Alignment identifier is 2/AL22
> sequence chain #2/AL23
Alignment identifier is 2/AL23
> sequence chain #2/AL24
Alignment identifier is 2/AL24
> sequence chain #2/AL25
Alignment identifier is 2/AL25
> sequence chain #2/AL26
Alignment identifier is 2/AL26
> sequence chain #2/AL27
Alignment identifier is 2/AL27
> sequence chain #2/AL28
Alignment identifier is 2/AL28
> sequence chain #2/AL29
Alignment identifier is 2/AL29
> sequence chain #2/AL30
Alignment identifier is 2/AL30
> sequence chain #2/AL31
Alignment identifier is 2/AL31
> sequence chain #2/AL32
Alignment identifier is 2/AL32
> sequence chain #2/AL33
Alignment identifier is 2/AL33
> sequence chain #2/AL34
Alignment identifier is 2/AL34
> sequence chain #2/AL35
Alignment identifier is 2/AL35
> sequence chain #2/AL36
Alignment identifier is 2/AL36
> sequence chain #2/AL37
Alignment identifier is 2/AL37
> sequence chain #2/AL38
Alignment identifier is 2/AL38
> sequence chain #2/AL39
Alignment identifier is 2/AL39
> sequence chain #2/AL40
Alignment identifier is 2/AL40
> sequence chain #2/AL41#4.57/Z
Alignment identifier is 5
> sequence chain #2/AL42
Alignment identifier is 2/AL42
> sequence chain #2/AL43
Alignment identifier is 2/AL43
> sequence chain #2/ALP0
Alignment identifier is 2/ALP0
> sequence chain #2/APTN
Alignment identifier is 2/APTN
> sequence chain #2/PR
Alignment identifier is 2/PR
> sequence chain #4.1/0
Alignment identifier is 4.1/0
> sequence chain #4.2/1
Alignment identifier is 4.2/1
> sequence chain #4.3/2
Alignment identifier is 4.3/2
> sequence chain #4.4/3
Alignment identifier is 4.4/3
> sequence chain #4.5/4
Alignment identifier is 4.5/4
> sequence chain #4.6/5
Alignment identifier is 4.6/5
> sequence chain #4.7/6
Alignment identifier is 4.7/6
> sequence chain #4.8/7
Alignment identifier is 4.8/7
> sequence chain #4.9/8
Alignment identifier is 4.9/8
> sequence chain #4.10/A
Alignment identifier is 4.10/A
> sequence chain #4.11/AA
Alignment identifier is 4.11/AA
> sequence chain #4.12/B
Alignment identifier is 4.12/B
> sequence chain #4.14/Bb
Alignment identifier is 4.14/Bb
> sequence chain #4.15/C
Alignment identifier is 4.15/C
> sequence chain #4.17/Cc
Alignment identifier is 4.17/Cc
> sequence chain #4.18/D
Alignment identifier is 4.18/D
> sequence chain #4.19/DD
Alignment identifier is 4.19/DD
> sequence chain #4.20/Dd
Alignment identifier is 4.20/Dd
> sequence chain #4.22/EE
Alignment identifier is 4.22/EE
> sequence chain #4.23/Ee
Alignment identifier is 4.23/Ee
> sequence chain #4.24/F
Alignment identifier is 4.24/F
> sequence chain #4.25/FF
Alignment identifier is 4.25/FF
> sequence chain #4.26/G
Alignment identifier is 4.26/G
> sequence chain #4.27/GG
Alignment identifier is 4.27/GG
> sequence chain #4.28/H
Alignment identifier is 4.28/H
> sequence chain #4.29/HH
Alignment identifier is 4.29/HH
> sequence chain #4.30/I
Alignment identifier is 4.30/I
> sequence chain #4.31/II
Alignment identifier is 4.31/II
> sequence chain #4.32/J
Alignment identifier is 4.32/J
> sequence chain #4.33/JJ
Alignment identifier is 4.33/JJ
> sequence chain #4.34/K
Alignment identifier is 4.34/K
> sequence chain #4.35/KK
Alignment identifier is 4.35/KK
> sequence chain #4.36/L
Alignment identifier is 4.36/L
> sequence chain #4.38/M
Alignment identifier is 4.38/M
> sequence chain #4.39/MM
Alignment identifier is 4.39/MM
> sequence chain #4.40/N
Alignment identifier is 4.40/N
> sequence chain #4.41/NN
Alignment identifier is 4.41/NN
> sequence chain #4.42/O
Alignment identifier is 4.42/O
> sequence chain #4.43/OO
Alignment identifier is 4.43/OO
> sequence chain #4.44/P
Alignment identifier is 4.44/P
> sequence chain #4.45/PP
Alignment identifier is 4.45/PP
> sequence chain #4.46/Pp
Alignment identifier is 4.46/Pp
> sequence chain #4.47/Q
Alignment identifier is 4.47/Q
> sequence chain #4.48/QQ
Alignment identifier is 4.48/QQ
> sequence chain #4.49/R
Alignment identifier is 4.49/R
> sequence chain #4.50/S
Alignment identifier is 4.50/S
> sequence chain #4.51/T
Alignment identifier is 4.51/T
> sequence chain #4.52/U
Alignment identifier is 4.52/U
> sequence chain #4.53/V
Alignment identifier is 4.53/V
> sequence chain #4.54/W
Alignment identifier is 4.54/W
> sequence chain #4.55/X
Alignment identifier is 4.55/X
> sequence chain #4.56/Y
Alignment identifier is 4.56/Y
> sequence chain #4.58/a
Alignment identifier is 4.58/a
> sequence chain #4.59/b
Alignment identifier is 4.59/b
> sequence chain #4.60/c
Alignment identifier is 4.60/c
> sequence chain #4.61/d
Alignment identifier is 4.61/d
> sequence chain #4.62/e
Alignment identifier is 4.62/e
> sequence chain #4.63/f
Alignment identifier is 4.63/f
> sequence chain #4.64/g
Alignment identifier is 4.64/g
> sequence chain #4.65/h
Alignment identifier is 4.65/h
> sequence chain #4.66/i
Alignment identifier is 4.66/i
> sequence chain #4.67/j
Alignment identifier is 4.67/j
> sequence chain #4.68/k
Alignment identifier is 4.68/k
> sequence chain #4.69/l
Alignment identifier is 4.69/l
> sequence chain #4.70/m
Alignment identifier is 4.70/m
> sequence chain #4.71/n
Alignment identifier is 4.71/n
> sequence chain #4.72/o
Alignment identifier is 4.72/o
> sequence chain #4.73/p
Alignment identifier is 4.73/p
> sequence chain #4.74/q
Alignment identifier is 4.74/q
> sequence chain #4.75/r
Alignment identifier is 4.75/r
> sequence chain #4.76/s
Alignment identifier is 4.76/s
> sequence chain #4.77/t
Alignment identifier is 4.77/t
> sequence chain #4.78/u
Alignment identifier is 4.78/u
> sequence chain #4.79/v
Alignment identifier is 4.79/v
> sequence chain #4.80/w
Alignment identifier is 4.80/w
> sequence chain #4.81/x
Alignment identifier is 4.81/x
> sequence chain #4.82/y
Alignment identifier is 4.82/y
> sequence chain #4.83/z
Alignment identifier is 4.83/z
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/zhangj14/My Drive/Cryo-
> EM/2025_Ribosomes/092625_K62_Krios/cryosparc_P52_J153_map_sharp.mrc"
Opened cryosparc_P52_J153_map_sharp.mrc as #1, grid size 512,512,512, pixel
0.93, shown at level 0.0831, step 2, values float32
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac13,1
Model Number: Z14J000H2LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 13822.61.10
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.3 (24G419)
Kernel Version: Darwin 24.6.0
Time since boot: 1 day, 3 hours, 40 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Studio Display:
Display Type: Retina LCD
Resolution: 5120 x 2880 Retina
Display Serial Number: JD71PFVWLJ
Display Firmware Version: Version 17.0 (Build 21A329)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 2 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash drawing widget while processing QGraphicsScene event |
comment:2 by , 2 weeks ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Crashed in Mac Metal graphics MTLReportFailure().