id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16232	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000000320653000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031f650000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031e64d000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031d64a000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031c647000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031b644000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031a641000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031963e000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031863b000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000317638000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000316635000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000315632000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031462f000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00000002024bf240 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, 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, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio (total: 55)


{""app_name"":""ChimeraX"",""timestamp"":""2024-10-30 18:24:02.00 +0100"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.6.1 (23G93)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""A752C1B0-45F6-436A-92D6-402BB70C288C""}
{
  ""uptime"" : 1200000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 502,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro18,3"",
  ""coalitionID"" : 203909,
  ""osVersion"" : {
    ""train"" : ""macOS 14.6.1"",
    ""build"" : ""23G93"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2024-10-30 18:23:06.1168 +0100"",
  ""codeSigningMonitor"" : 1,
  ""incident"" : ""A752C1B0-45F6-436A-92D6-402BB70C288C"",
  ""pid"" : 50363,
  ""translated"" : true,
  ""cpuType"" : ""X86-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2024-10-30 08:48:57.3201 +0100"",
  ""procStartAbsTime"" : 28099591544862,
  ""procExitAbsTime"" : 28912957935271,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"",
  ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""},
  ""storeInfo"" : {""deviceIdentifierForVendor"":""B4DDC594-132A-5603-829D-C01C2C235676"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""4C8E28A8-55FD-C00A-23DC-2343A29F27E7"",
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 4294967295,
  ""wakeTime"" : 31571,
  ""sleepWakeUUID"" : ""950AFC03-2E29-44E2-8483-1E760CA6B2B7"",
  ""sip"" : ""enabled"",
  ""vmRegionInfo"" : ""0x2dad1f9db398 is not in any region.  Bytes after previous region: 49740546683801  Bytes before following region: 55331533245544\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, 0x00002dad1f9db398"",""rawCodes"":[1,50221583020952],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00002dad1f9db398""},
  ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":50363},
  ""vmregioninfo"" : ""0x2dad1f9db398 is not in any region.  Bytes after previous region: 49740546683801  Bytes before following region: 55331533245544\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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      ""rolloutId"" : ""6112d17137f5d11121dcd4e2"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000570
    },
    {
      ""rolloutId"" : ""63508950b3714d3622fc77f7"",
      ""factorPackIds"" : {
        ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8""
      },
      ""deploymentId"" : 240000015
    }
  ],
  ""experiments"" : [
    {
      ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"",
      ""experimentId"" : ""6643969b3099cf28e049862f"",
      ""deploymentId"" : 400000007
    }
  ]
},
  ""reportNotes"" : [
  ""PC register does not match crashing frame (0x0 vs 0x7FF8A8E06A78)""
]
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/roan.groh/Downloads/cryosparc_P541_J57_class_09_00149_volume.mrc

Opened cryosparc_P541_J57_class_09_00149_volume.mrc as #1, grid size
120,120,120, pixel 3.8, shown at level 0.983, step 1, values float32  

> open /Users/roan.groh/Downloads/cryosparc_P541_J57_class_07_00149_volume.mrc

Opened cryosparc_P541_J57_class_07_00149_volume.mrc as #2, grid size
120,120,120, pixel 3.8, shown at level 1.08, step 1, values float32  

> open /Users/roan.groh/Downloads/cryosparc_P541_J57_class_06_00149_volume.mrc

Opened cryosparc_P541_J57_class_06_00149_volume.mrc as #3, grid size
120,120,120, pixel 3.8, shown at level 0.998, step 1, values float32  

> open /Users/roan.groh/Downloads/cryosparc_P541_J57_class_05_00149_volume.mrc

Opened cryosparc_P541_J57_class_05_00149_volume.mrc as #4, grid size
120,120,120, pixel 3.8, shown at level 1, step 1, values float32  

> open /Users/roan.groh/Downloads/cryosparc_P541_J57_class_04_00149_volume.mrc

Opened cryosparc_P541_J57_class_04_00149_volume.mrc as #5, grid size
120,120,120, pixel 3.8, shown at level 1.07, step 1, values float32  

> open /Users/roan.groh/Downloads/cryosparc_P541_J57_class_01_00149_volume.mrc

Opened cryosparc_P541_J57_class_01_00149_volume.mrc as #6, grid size
120,120,120, pixel 3.8, shown at level 1.02, step 1, values float32  

> open /Users/roan.groh/Downloads/cryosparc_P541_J57_class_00_00149_volume.mrc

Opened cryosparc_P541_J57_class_00_00149_volume.mrc as #7, grid size
120,120,120, pixel 3.8, shown at level 1.02, step 1, values float32  

> hide #!1 models

> hide #!2 models

> hide #!4 models

> hide #!6 models

> hide #!7 models

> hide #!5 models

> volume #3 level 0.2031

> hide #!3 models

> show #!6 models

> show #!4 models

> volume #4 level 0.9481

> volume #6 level 0.9892

> volume #6 level 0.8729

> hide #!4 models

> hide #!6 models

> vop gaussian #7 sDev 2

Opened cryosparc_P541_J57_class_00_00149_volume.mrc gaussian as #8, grid size
120,120,120, pixel 3.8, shown at step 1, values float32  

> hide #!8 models

> vop gaussian #6 sDev 2

Opened cryosparc_P541_J57_class_01_00149_volume.mrc gaussian as #9, grid size
120,120,120, pixel 3.8, shown at step 1, values float32  

> vop gaussian #5 sDev 2

Opened cryosparc_P541_J57_class_04_00149_volume.mrc gaussian as #10, grid size
120,120,120, pixel 3.8, shown at step 1, values float32  

> vop gaussian #4 sDev 2

Opened cryosparc_P541_J57_class_05_00149_volume.mrc gaussian as #11, grid size
120,120,120, pixel 3.8, shown at step 1, values float32  

> vop gaussian #3 sDev 2

Opened cryosparc_P541_J57_class_06_00149_volume.mrc gaussian as #12, grid size
120,120,120, pixel 3.8, shown at step 1, values float32  

> vop gaussian #2 sDev 2

Opened cryosparc_P541_J57_class_07_00149_volume.mrc gaussian as #13, grid size
120,120,120, pixel 3.8, shown at step 1, values float32  

> vop gaussian #1 sDev 2

Opened cryosparc_P541_J57_class_09_00149_volume.mrc gaussian as #14, grid size
120,120,120, pixel 3.8, shown at step 1, values float32  

> show #!8 models

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!14 models

> show #!14 models

> hide #!13 models

> hide #!14 models

> volume #8 level 0.3158

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

> open 8b2l

Summary of feedback from opening 8b2l fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /k1:1  
Atom H1 is not in the residue template for MET /G1:1  
Atom H1 is not in the residue template for MET /D3:1  
Atom H1 is not in the residue template for MET /p3:1  
Atom H1 is not in the residue template for MET /m3:1  
2 messages similar to the above omitted  
  
8b2l title:  
Cryo-EM structure of the plant 80S ribosome [more info...]  
  
Chain information for 8b2l #15  
---  
Chain | Description | UniProt  
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264  
A3 | 25S rRNA |   
B1 | mRNA |   
B3 | 5.8S rRNA |   
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144  
C3 | 5S rRNA |   
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149  
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206  
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143  
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134  
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261  
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204  
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83  
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187  
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133  
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214  
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107  
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178  
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127  
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164  
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86  
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127  
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65  
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164  
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62  
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135  
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156  
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143  
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191  
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61  
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224  
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113  
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329  
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120  
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122  
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133  
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150  
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112  
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142  
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120  
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152  
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110  
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56  
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95  
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151  
W2 i2 | tRNA |   
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69  
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159  
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51  
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152  
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128  
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336  
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105  
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248  
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92  
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197  
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230  
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280  
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258  
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210  
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206  
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130  
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140  
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150  
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148  
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221  
h1 | 18S rRNA |   
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301  
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175  
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249  
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154  
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208  
l3 | nascent chain |   
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146  
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123  
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260  
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25  
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242  
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389  
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405  
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181  
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194  
  
Non-standard residues in 8b2l #15  
---  
1MA — 6-hydro-1-methyladenosine-5'-monophosphate  
4AC — N(4)-acetylcytidine-5'-monophosphate  
5MC — 5-methylcytidine-5'-monophosphate  
6MZ — N6-methyladenosine-5'-monophosphate  
A2M — 2'-O-methyladenosine 5'-(dihydrogen phosphate)  
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  
MA6 — 6N-dimethyladenosine-5'-monophoshate  
MG — magnesium ion  
OMC — O2'-methylycytidine-5'-monophosphate  
OMG — O2'-methylguanosine-5'-monophosphate  
OMU — O2'-methyluridine 5'-monophosphate  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
SPM — spermine  
UR3 — 3-methyluridine-5'-monophoshate  
UY1 — 2'-O-methylpseudouridine-5'-monophosphate  
ZN — zinc ion  
  

> select add #15

361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected  

> hide sel atoms

> show sel cartoons

> ui mousemode right ""translate selected models""

> view matrix models #15,1,0,0,95.424,0,1,0,-196.54,0,0,1,84.236

> ui mousemode right ""rotate selected models""

> view matrix models
> #15,0.09828,0.03507,0.99454,82.686,0.50685,0.85828,-0.080352,-263.18,-0.85642,0.51198,0.066577,361.66

> view matrix models
> #15,0.41976,0.40856,0.81049,-10.221,0.178,0.83857,-0.5149,-105.86,-0.89001,0.3604,0.27927,352.02

> ui mousemode right ""translate selected models""

> view matrix models
> #15,0.41976,0.40856,0.81049,-1.93,0.178,0.83857,-0.5149,125.12,-0.89001,0.3604,0.27927,256.3

> view matrix models
> #15,0.41976,0.40856,0.81049,-90.094,0.178,0.83857,-0.5149,161.57,-0.89001,0.3604,0.27927,267.08

> view matrix models
> #15,0.41976,0.40856,0.81049,-105.35,0.178,0.83857,-0.5149,145.3,-0.89001,0.3604,0.27927,280.9

> view matrix models
> #15,0.41976,0.40856,0.81049,-98.519,0.178,0.83857,-0.5149,127.91,-0.89001,0.3604,0.27927,286.62

> view matrix models
> #15,0.41976,0.40856,0.81049,-92.548,0.178,0.83857,-0.5149,122.29,-0.89001,0.3604,0.27927,285.36

> hide #!8 models

> show #!7 models

> volume #7 level 0.3193

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

> fitmap #15 inMap #7

Fit molecule 8b2l (#15) to map cryosparc_P541_J57_class_00_00149_volume.mrc
(#7) using 361205 atoms  
average map value = 0.5817, steps = 76  
shifted from previous position = 11.8  
rotated from previous position = 4.96 degrees  
atoms outside contour = 106903, contour level = 0.31932  
  
Position of 8b2l (#15) relative to
cryosparc_P541_J57_class_00_00149_volume.mrc (#7) coordinates:  
Matrix rotation and translation  
0.49026070 0.42175656 0.76273577 -92.73557285  
0.14929642 0.82155060 -0.55024104 146.62985296  
-0.85869379 0.38363527 0.33980723 260.04130260  
Axis 0.49388683 0.85750404 -0.14409240  
Axis point 129.03948607 0.00000000 235.31726487  
Rotation angle (degrees) 70.98538894  
Shift along axis 42.46483778  
  

> hide #!7 models

> show #!8 models

> select subtract #15

Nothing selected  

> hide #!15 models

> view #15 clip false

No displayed objects specified.  

> select add #8

2 models selected  

> view #15 clip false

No displayed objects specified.  

> show #!15 target m

> select subtract #8

Nothing selected  

> hide #!15 models

> view #8 clip false

> lighting soft

> ui tool show ""Side View""

> show #!9 models

> hide #!8 models

> volume #9 level 0.3054

> hide #!9 models

> show #!10 models

> volume #10 level 0.3378

> volume #10 level 0.2121

> hide #!10 models

> show #!11 models

> volume #11 level 0.1867

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!8 models

> hide #!11 models

> show #!12 models

> volume #12 level 0.3457

> hide #!12 models

> show #!13 models

> volume #13 level 0.3144

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> select add #14

2 models selected  

> select subtract #14

Nothing selected  

> show #!14 models

> hide #!13 models

> volume #14 level 0.2829

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!12 models

> hide #!12 models

> show #!11 models

> hide #!11 models

> show #!10 models

> hide #!10 models

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!8 models

> show #!14 target m

> view #14 clip false

> show #!15 models

> log metadata #15

Metadata for 8b2l #15  
---  
Title | Cryo-EM structure of the plant 80S ribosome  
Citation | Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Burger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.M.T., Zoschke, R. (2023). Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat.Plants, 9, 987-1000. PMID: 37156858. DOI: 10.1038/s41477-023-01407-y  
Non-standard residues | 1MA — 6-hydro-1-methyladenosine-5'-monophosphate  
4AC — N(4)-acetylcytidine-5'-monophosphate  
5MC — 5-methylcytidine-5'-monophosphate  
6MZ — N6-methyladenosine-5'-monophosphate  
A2M — 2'-O-methyladenosine 5'-(dihydrogen phosphate)  
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  
MA6 — 6N-dimethyladenosine-5'-monophoshate  
MG — magnesium ion  
OMC — O2'-methylycytidine-5'-monophosphate  
OMG — O2'-methylguanosine-5'-monophosphate  
OMU — O2'-methyluridine 5'-monophosphate  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
SPM — spermine  
UR3 — 3-methyluridine-5'-monophoshate  
UY1 — 2'-O-methylpseudouridine-5'-monophosphate  
ZN — zinc ion  
Sources (natural) | Nicotiana tabacum  
Nicotiana tabacum (common tobacco)  
CryoEM Map | EMDB 15806 — open map  
Experimental method | Electron microscopy  
Resolution | 2.20Å  
  
> log chains #15

Chain information for 8b2l #15  
---  
Chain | Description | UniProt  
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264  
A3 | 25S rRNA |   
B1 | mRNA |   
B3 | 5.8S rRNA |   
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144  
C3 | 5S rRNA |   
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149  
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206  
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143  
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134  
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261  
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204  
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83  
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187  
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133  
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214  
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107  
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178  
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127  
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164  
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86  
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127  
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65  
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164  
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62  
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135  
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156  
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143  
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191  
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61  
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224  
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113  
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329  
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120  
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122  
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133  
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150  
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112  
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142  
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120  
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152  
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110  
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56  
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95  
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151  
W2 i2 | tRNA |   
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69  
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159  
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51  
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152  
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128  
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336  
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105  
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248  
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92  
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197  
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230  
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280  
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258  
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210  
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206  
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130  
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140  
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150  
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148  
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221  
h1 | 18S rRNA |   
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301  
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175  
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249  
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154  
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208  
l3 | nascent chain |   
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146  
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123  
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260  
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25  
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242  
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389  
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405  
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181  
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194  
  

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> log metadata #15

Metadata for 8b2l #15  
---  
Title | Cryo-EM structure of the plant 80S ribosome  
Citation | Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Burger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.M.T., Zoschke, R. (2023). Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat.Plants, 9, 987-1000. PMID: 37156858. DOI: 10.1038/s41477-023-01407-y  
Non-standard residues | 1MA — 6-hydro-1-methyladenosine-5'-monophosphate  
4AC — N(4)-acetylcytidine-5'-monophosphate  
5MC — 5-methylcytidine-5'-monophosphate  
6MZ — N6-methyladenosine-5'-monophosphate  
A2M — 2'-O-methyladenosine 5'-(dihydrogen phosphate)  
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  
MA6 — 6N-dimethyladenosine-5'-monophoshate  
MG — magnesium ion  
OMC — O2'-methylycytidine-5'-monophosphate  
OMG — O2'-methylguanosine-5'-monophosphate  
OMU — O2'-methyluridine 5'-monophosphate  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
SPM — spermine  
UR3 — 3-methyluridine-5'-monophoshate  
UY1 — 2'-O-methylpseudouridine-5'-monophosphate  
ZN — zinc ion  
Sources (natural) | Nicotiana tabacum  
Nicotiana tabacum (common tobacco)  
CryoEM Map | EMDB 15806 — open map  
Experimental method | Electron microscopy  
Resolution | 2.20Å  
  
> log chains #15

Chain information for 8b2l #15  
---  
Chain | Description | UniProt  
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264  
A3 | 25S rRNA |   
B1 | mRNA |   
B3 | 5.8S rRNA |   
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144  
C3 | 5S rRNA |   
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149  
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206  
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143  
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134  
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261  
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204  
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83  
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187  
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133  
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214  
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107  
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178  
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127  
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164  
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86  
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127  
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65  
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164  
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62  
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135  
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156  
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143  
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191  
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61  
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224  
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113  
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329  
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120  
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122  
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133  
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150  
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112  
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142  
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120  
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152  
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110  
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56  
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95  
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151  
W2 i2 | tRNA |   
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69  
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159  
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51  
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152  
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128  
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336  
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105  
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248  
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92  
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197  
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230  
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280  
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258  
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210  
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206  
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130  
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140  
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150  
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148  
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221  
h1 | 18S rRNA |   
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301  
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175  
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249  
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154  
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208  
l3 | nascent chain |   
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146  
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123  
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260  
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25  
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242  
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389  
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405  
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181  
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194  
  

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> log metadata #15

Metadata for 8b2l #15  
---  
Title | Cryo-EM structure of the plant 80S ribosome  
Citation | Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Burger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.M.T., Zoschke, R. (2023). Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat.Plants, 9, 987-1000. PMID: 37156858. DOI: 10.1038/s41477-023-01407-y  
Non-standard residues | 1MA — 6-hydro-1-methyladenosine-5'-monophosphate  
4AC — N(4)-acetylcytidine-5'-monophosphate  
5MC — 5-methylcytidine-5'-monophosphate  
6MZ — N6-methyladenosine-5'-monophosphate  
A2M — 2'-O-methyladenosine 5'-(dihydrogen phosphate)  
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  
MA6 — 6N-dimethyladenosine-5'-monophoshate  
MG — magnesium ion  
OMC — O2'-methylycytidine-5'-monophosphate  
OMG — O2'-methylguanosine-5'-monophosphate  
OMU — O2'-methyluridine 5'-monophosphate  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
SPM — spermine  
UR3 — 3-methyluridine-5'-monophoshate  
UY1 — 2'-O-methylpseudouridine-5'-monophosphate  
ZN — zinc ion  
Sources (natural) | Nicotiana tabacum  
Nicotiana tabacum (common tobacco)  
CryoEM Map | EMDB 15806 — open map  
Experimental method | Electron microscopy  
Resolution | 2.20Å  
  
> log chains #15

Chain information for 8b2l #15  
---  
Chain | Description | UniProt  
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264  
A3 | 25S rRNA |   
B1 | mRNA |   
B3 | 5.8S rRNA |   
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144  
C3 | 5S rRNA |   
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149  
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206  
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143  
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134  
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261  
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204  
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83  
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187  
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133  
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214  
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107  
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178  
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127  
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164  
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86  
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127  
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65  
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164  
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62  
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135  
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156  
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143  
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191  
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61  
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224  
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113  
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329  
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120  
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122  
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133  
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150  
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112  
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142  
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120  
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152  
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110  
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56  
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95  
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151  
W2 i2 | tRNA |   
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69  
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159  
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51  
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152  
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128  
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336  
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105  
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248  
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92  
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197  
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230  
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280  
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258  
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210  
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206  
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130  
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140  
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150  
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148  
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221  
h1 | 18S rRNA |   
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301  
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175  
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249  
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154  
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208  
l3 | nascent chain |   
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146  
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123  
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260  
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25  
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242  
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389  
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405  
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181  
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194  
  

> volume #4 level 0.1117

> hide #!15 models

> hide #!4 models

> show #!3 models

> show #!12 models

> volume #12 level 0.1567

> hide #!12 models

> hide #!3 models

> show #!2 models

> volume #2 level 0.2417

> show #!15 models

> hide #!2 models

> show #!1 models

> volume #1 level 0.2311

> hide #!1 models

> hide #!8 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> color #8 #e5bf99ff models

> show #!8 models

> show #!1 models

> hide #!8 models

> ui tool show ""Side View""

> view #8 clip false

No displayed objects specified.  

> view #1 clip false

> hide #!1 models

> show #!7 models

> volume #7 level 0.2558

> hide #!7 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!4 models

> view #4 clip false

> volume #4 level 0.2564

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!6 models

> show #!15 models

> hide #!15 models

> show #!5 models

> hide #!5 models

> show #!3 models

> hide #!4 models

> volume #3 level 0.2472

> hide #!3 models

> show #!2 models

> view #6 clip false

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!2 models

> show #!1 models

> show #!4 models

> show #!2 models

> show #!3 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!7 models

> hide #!7 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> hide #!6 models

> show #!8 models

> show #!9 models

> show #!10 models

> show #!11 models

> hide #!10 models

> show #!12 models

> show #!13 models

> show #!14 models

> view #9 clip false

> volume #1 level 0.1161

> volume #2 level 0.2333

> volume #8 level 0.06156

> volume #9 level 0.05024

> volume #11 level 0.05087

> volume #12 level 0.06494

> volume #13 level 0.0695

> volume #14 level 0.06145

> hide #!9 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> show #!15 models

> hide #!15 models

> color #8 #e5bf997b models

> color #8 #e5bf997a models

> show #!15 models

> hide #!15 models

> hide #!8 models

> show #!11 models

> show #!14 models

> view #14 clip false

> volume #4 level 0.2484

> volume #4 level 0.4334

> volume #14 level 0.3798

> volume #14 level 0.2829

> volume #11 level 0.1165

> hide #!4 models

> volume #14 level 0.1953

> show #!1 models

> hide #!14 models

> volume #1 level 0.2081

> view clip false

> volume #1 level 0.4229

> volume #1 level 0.3769

> volume #1 level 0.3078

> volume #1 level 0.2235

> volume #1 level 0.1851

> open /Users/roan.groh/Downloads/cryosparc_P541_J59_class_04_00024_volume.mrc

Opened cryosparc_P541_J59_class_04_00024_volume.mrc as #16, grid size
160,160,160, pixel 2.85, shown at level 0.78, step 1, values float32  

> open /Users/roan.groh/Downloads/cryosparc_P541_J59_class_00_00024_volume.mrc

Opened cryosparc_P541_J59_class_00_00024_volume.mrc as #17, grid size
160,160,160, pixel 2.85, shown at level 0.754, step 1, values float32  

> hide #!1 models

> volume #16 level 0.3584

> volume #17 level 0.4124

> ui tool show ""Side View""

> vop gaussian #16 sDev 2

Opened cryosparc_P541_J59_class_04_00024_volume.mrc gaussian as #18, grid size
160,160,160, pixel 2.85, shown at step 1, values float32  

> vop gaussian #17 sDev 2

Opened cryosparc_P541_J59_class_00_00024_volume.mrc gaussian as #19, grid size
160,160,160, pixel 2.85, shown at step 1, values float32  

> volume #18 level 0.1398

> volume #19 level 0.1689

> color #18 #b2ffb280 models

> hide #!19 models

> show #!16 models

> hide #!16 models

> show #!17 models

> volume #17 level 0.4124


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

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




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

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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGT3D/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 47 days, 22 hours, 28 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP Z27n G2:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 75.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX