id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16224	Graphics crash, macOS 14.6.1, Intel Iris Plus Graphics 645	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: Aborted

Thread 0x000070000fcea000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 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 0x000070001af17000 (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 0x0000700019f14000 (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 0x0000700018f11000 (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 0x0000700017f0e000 (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 0x0000700016f0b000 (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 0x0000700015f08000 (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 0x0000700014f05000 (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 0x0000700013f02000 (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 0x0000700012eff000 (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 0x0000700011efc000 (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 0x0000700010ef9000 (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 0x00007ff85695adc0 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 556 in swap_buffers
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 202 in draw
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback
  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.pdb_lib._load_libs, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 123)


{""app_name"":""ChimeraX"",""timestamp"":""2024-10-31 09:52:19.00 -0700"",""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"":""5BABA70A-45BE-426E-A04B-EEE045D4AE16""}
{
  ""uptime"" : 110000,
  ""procRole"" : ""Foreground"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro15,4"",
  ""coalitionID"" : 11477,
  ""osVersion"" : {
    ""train"" : ""macOS 14.6.1"",
    ""build"" : ""23G93"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2024-10-31 09:51:44.8594 -0700"",
  ""codeSigningMonitor"" : 0,
  ""incident"" : ""5BABA70A-45BE-426E-A04B-EEE045D4AE16"",
  ""pid"" : 76424,
  ""cpuType"" : ""X86-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2024-10-30 14:15:26.0762 -0700"",
  ""procStartAbsTime"" : 78740582607222,
  ""procExitAbsTime"" : 112597077723793,
  ""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"":""FE8593A6-1515-525E-BBE3-7E5F38F75251"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""CA3597E7-7DF9-8A23-33FE-0342FDD4E3EF"",
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 4294967295,
  ""wakeTime"" : 315,
  ""bridgeVersion"" : {""build"":""21P6074"",""train"":""8.6""},
  ""sleepWakeUUID"" : ""2B2C173D-27A6-4756-9DAD-B77965DB76C8"",
  ""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"":76424},
  ""asi"" : {""libsystem_c.dylib"":[""abort() called""]},
  ""asiSignatures"" : [""Graphics hardware encountered an error and was reset: 0x00000002\n""],
  ""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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===== 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  

> ui tool show Registration

> open /Users/julianaabramovich/Downloads/model_aligned_wQ8.cif format mmcif

Summary of feedback from opening
/Users/julianaabramovich/Downloads/model_aligned_wQ8.cif  
---  
warnings | Atom HO5' is not in the residue template for C /L5:1  
Atom HO5' is not in the residue template for C /L8:1  
Atom HO5' is not in the residue template for U /S2:1  
  
Chain information for model_aligned_wQ8.cif #1  
---  
Chain | Description  
1 | nascent chain  
CC | tRNA  
L5 | 28S ribosomal RNA  
L7 | 5S ribosomal RNA  
L8 | 5.8S ribosomal RNA  
LA | 60S ribosomal protein L8  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4  
LD | 60S ribosomal protein L5  
LE | MAGNESIUM ION  
LF | 60S ribosomal protein L7  
LG | 60S ribosomal protein L7a  
LH | 60S ribosomal protein L9  
LI | 60S ribosomal protein L10-like  
LJ | 60S ribosomal protein L11  
LL | 60S ribosomal protein L13  
LM | 60S ribosomal protein L14  
LN | 60S ribosomal protein L15  
LO | 60S ribosomal protein L13a  
LP | 60S ribosomal protein L17  
LQ | 60S ribosomal protein L18  
LR | 60S ribosomal protein L19  
LS | No description available  
LT | 60S ribosomal protein L21  
LU | 60S ribosomal protein L22  
LV | 60S ribosomal protein L23  
LW | 60S ribosomal protein L24  
LX | 60S ribosomal protein L23a  
LY | 60S ribosomal protein L26  
LZ | 60S ribosomal protein L27  
La | 60S ribosomal protein L27a  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L35a  
Lg | 60S ribosomal protein L34  
Lh | 60S ribosomal protein L35  
Li | 60S ribosomal protein L36  
Lj | 60S ribosomal protein L37  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | Ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41  
Lo | 60S ribosomal protein L36a  
Lp | 60S ribosomal protein L37a  
Lr | 60S ribosomal protein L28  
Ls | 60S acidic ribosomal protein P0  
Lt | 60S ribosomal protein L12  
Lz | 60S ribosomal protein L10a  
S2 | 18S ribosomal RNA  
SA | 60S ribosomal protein L28  
SB | 40S ribosomal protein S3a  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15a  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
Sf | Ubiquitin-40S ribosomal protein S27a  
Sg | Receptor of activated protein C kinase 1  
v | tRNA  
w | mRNA  
  

> open
> /Users/julianaabramovich/Downloads/cryosparc_P120_J258_007_volume_map.mrc
> /Users/julianaabramovich/Downloads/cryosparc_P120_J257_006_volume_map.mrc
> /Users/julianaabramovich/Downloads/cryosparc_P120_J256_008_volume_map.mrc
> /Users/julianaabramovich/Downloads/cryosparc_P120_J255_007_volume_map.mrc

Opened cryosparc_P120_J258_007_volume_map.mrc as #2.1, grid size 512,512,512,
pixel 1.03, shown at level 0.197, step 2, values float32  
Opened cryosparc_P120_J257_006_volume_map.mrc as #2.2, grid size 512,512,512,
pixel 1.03, shown at level 0.208, step 2, values float32  
Opened cryosparc_P120_J256_008_volume_map.mrc as #2.3, grid size 512,512,512,
pixel 1.03, shown at level 0.204, step 2, values float32  
Opened cryosparc_P120_J255_007_volume_map.mrc as #2.4, grid size 512,512,512,
pixel 1.03, shown at level 0.202, step 2, values float32  

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

> surface dust #2.1 size 10.3

> surface dust #2.2 size 10.3

> surface dust #2.3 size 10.3

> surface dust #2.4 size 10.3

> select add #1

387692 atoms, 404232 bonds, 137 pseudobonds, 17924 residues, 4 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #1,1,0,0,-280.16,0,1,0,-18.78,0,0,1,19.889

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.72616,-0.51632,0.454,-191.47,-0.44173,0.15565,0.88354,85.69,-0.52686,-0.84213,-0.11504,698.05

> view matrix models
> #1,0.70842,-0.70428,-0.046195,2.9379,-0.3778,-0.43368,0.81804,248.76,-0.59616,-0.56206,-0.5733,765.96

> view matrix models
> #1,0.6359,-0.47237,-0.61032,114.15,-0.30981,-0.88054,0.35871,480.36,-0.70686,-0.039025,-0.70628,688.24

> view matrix models
> #1,0.42812,0.32962,-0.84146,12.544,0.55745,-0.82919,-0.04119,347.85,-0.71131,-0.45144,-0.53874,756.42

> view matrix models
> #1,0.3799,0.73198,-0.56558,-161.41,0.83859,-0.01446,0.54457,-111.81,0.39044,-0.68117,-0.61933,551.06

> view matrix models
> #1,0.52625,0.73873,-0.42111,-241.77,0.75815,-0.18337,0.62576,-66.618,0.38505,-0.64857,-0.65657,553.81

> view matrix models
> #1,0.89426,0.32061,-0.31227,-254.09,0.40955,-0.86758,0.28208,308.16,-0.18049,-0.38014,-0.90715,698.5

> view matrix models
> #1,0.9964,-0.042297,-0.073408,-247.33,-0.015218,-0.94172,0.33605,425.69,-0.083344,-0.33373,-0.93898,668.91

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.9964,-0.042297,-0.073408,91.632,-0.015218,-0.94172,0.33605,490.88,-0.083344,-0.33373,-0.93898,673.72

> view matrix models
> #1,0.9964,-0.042297,-0.073408,-26.084,-0.015218,-0.94172,0.33605,426.99,-0.083344,-0.33373,-0.93898,653.2

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.97557,0.0055908,0.21963,-114.65,-0.059259,-0.95593,0.28756,455.9,0.21155,-0.29355,-0.93224,562.5

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.97557,0.0055908,0.21963,-73.644,-0.059259,-0.95593,0.28756,472.26,0.21155,-0.29355,-0.93224,538.24

> ui tool show ""Fit in Map""

> fitmap #1 inMap #2.1

Fit molecule model_aligned_wQ8.cif (#1) to map
cryosparc_P120_J258_007_volume_map.mrc (#2.1) using 387692 atoms  
average map value = 0.205, steps = 2000  
shifted from previous position = 25.9  
rotated from previous position = 21.4 degrees  
atoms outside contour = 236989, contour level = 0.19738  
  
Position of model_aligned_wQ8.cif (#1) relative to
cryosparc_P120_J258_007_volume_map.mrc (#2.1) coordinates:  
Matrix rotation and translation  
0.99830399 0.05765453 0.00806924 -16.06294680  
0.05763147 -0.99833323 0.00306308 514.49516107  
0.00823238 -0.00259284 -0.99996275 528.58236604  
Axis -0.99957593 -0.02883295 -0.00407627  
Axis point 0.00000000 257.85326705 263.95990249  
Rotation angle (degrees) 179.83790106  
Shift along axis -0.93292368  
  

> ui mousemode right ""translate selected models""

> ui mousemode right select

> select clear

> select /w

318 atoms, 341 bonds, 10 residues, 1 model selected  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

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

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 7 residues in model #1 to IUPAC-IUB
standards.  
Chain information for model_aligned_wQ8.cif  
---  
Chain | Description  
1.2/1 | nascent chain  
1.2/CC | tRNA  
1.2/L5 | 28S ribosomal RNA  
1.2/L7 | 5S ribosomal RNA  
1.2/L8 | 5.8S ribosomal RNA  
1.2/LA | 60S ribosomal protein L8  
1.2/LB | 60S ribosomal protein L3  
1.2/LC | 60S ribosomal protein L4  
1.2/LD | 60S ribosomal protein L5  
1.2/LE | MAGNESIUM ION  
1.2/LF | 60S ribosomal protein L7  
1.2/LG | 60S ribosomal protein L7a  
1.2/LH | 60S ribosomal protein L9  
1.2/LI | 60S ribosomal protein L10-like  
1.2/LJ | 60S ribosomal protein L11  
1.2/LL | 60S ribosomal protein L13  
1.2/LM | 60S ribosomal protein L14  
1.2/LN | 60S ribosomal protein L15  
1.2/LO | 60S ribosomal protein L13a  
1.2/LP | 60S ribosomal protein L17  
1.2/LQ | 60S ribosomal protein L18  
1.2/LR | 60S ribosomal protein L19  
1.2/LS | No description available  
1.2/LT | 60S ribosomal protein L21  
1.2/LU | 60S ribosomal protein L22  
1.2/LV | 60S ribosomal protein L23  
1.2/LW | 60S ribosomal protein L24  
1.2/LX | 60S ribosomal protein L23a  
1.2/LY | 60S ribosomal protein L26  
1.2/LZ | 60S ribosomal protein L27  
1.2/La | 60S ribosomal protein L27a  
1.2/Lb | 60S ribosomal protein L29  
1.2/Lc | 60S ribosomal protein L30  
1.2/Ld | 60S ribosomal protein L31  
1.2/Le | 60S ribosomal protein L32  
1.2/Lf | 60S ribosomal protein L35a  
1.2/Lg | 60S ribosomal protein L34  
1.2/Lh | 60S ribosomal protein L35  
1.2/Li | 60S ribosomal protein L36  
1.2/Lj | 60S ribosomal protein L37  
1.2/Lk | 60S ribosomal protein L38  
1.2/Ll | 60S ribosomal protein L39  
1.2/Lm | Ubiquitin-60S ribosomal protein L40  
1.2/Ln | 60S ribosomal protein L41  
1.2/Lo | 60S ribosomal protein L36a  
1.2/Lp | 60S ribosomal protein L37a  
1.2/Lr | 60S ribosomal protein L28  
1.2/Ls | 60S acidic ribosomal protein P0  
1.2/Lt | 60S ribosomal protein L12  
1.2/Lz | 60S ribosomal protein L10a  
1.2/S2 | 18S ribosomal RNA  
1.2/SA | 60S ribosomal protein L28  
1.2/SB | 40S ribosomal protein S3a  
1.2/SC | 40S ribosomal protein S2  
1.2/SD | 40S ribosomal protein S3  
1.2/SE | 40S ribosomal protein S4, X isoform  
1.2/SF | 40S ribosomal protein S5  
1.2/SG | 40S ribosomal protein S6  
1.2/SH | 40S ribosomal protein S7  
1.2/SI | 40S ribosomal protein S8  
1.2/SJ | 40S ribosomal protein S9  
1.2/SK | 40S ribosomal protein S10  
1.2/SL | 40S ribosomal protein S11  
1.2/SM | 40S ribosomal protein S12  
1.2/SN | 40S ribosomal protein S13  
1.2/SO | 40S ribosomal protein S14  
1.2/SP | 40S ribosomal protein S15  
1.2/SQ | 40S ribosomal protein S16  
1.2/SR | 40S ribosomal protein S17  
1.2/SS | 40S ribosomal protein S18  
1.2/ST | 40S ribosomal protein S19  
1.2/SU | 40S ribosomal protein S20  
1.2/SV | 40S ribosomal protein S21  
1.2/SW | 40S ribosomal protein S15a  
1.2/SX | 40S ribosomal protein S23  
1.2/SY | 40S ribosomal protein S24  
1.2/SZ | 40S ribosomal protein S25  
1.2/Sa | 40S ribosomal protein S26  
1.2/Sb | 40S ribosomal protein S27  
1.2/Sc | 40S ribosomal protein S28  
1.2/Sd | 40S ribosomal protein S29  
1.2/Se | 40S ribosomal protein S30  
1.2/Sf | Ubiquitin-40S ribosomal protein S27a  
1.2/Sg | Receptor of activated protein C kinase 1  
1.2/v | tRNA  
1.2/w | mRNA  
  

> clipper associate #2.4 toModel #1

Opened cryosparc_P120_J255_007_volume_map.mrc as #1.1.1.1, grid size
512,512,512, pixel 1.03, shown at step 1, values float32  

> select /w

318 atoms, 341 bonds, 10 residues, 1 model selected  

> view sel

Drag select of 1 bonds  
Drag select of 1 atoms, 2 residues  

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

> volume #1.1.1.1 style surface

> volume #1.1.1.1 level 0.297

> volume #1.1.1.1 level 0.3518

> select /w:18@N7

1 atom, 1 residue, 1 model selected  

> volume #1.1.1.1 level 0.2941

> volume #2.1 level 0.2896

> select ~sel & ##selected

387691 atoms, 404232 bonds, 137 pseudobonds, 17924 residues, 4 models selected  

> volume #2.2 level 0.3408

> clipper associate #2.1 toModel #1

Opened cryosparc_P120_J258_007_volume_map.mrc as #1.1.1.2, grid size
512,512,512, pixel 1.03, shown at step 1, values float32  

> volume #1.1.1.2 color #7aff51

> volume #1.1.1.2 color #fea5ff

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

> volume #1.1.1.2 style surface

> volume #1.1.1.2 level 0.3645

> volume #1.1.1.2 level 0.3112

> volume #1.1.1.1 level 0.3265

> volume #1.1.1.2 level 0.3503

> volume #1.1.1.2 level 0.3254

> volume #1.1.1.2 level 0.4677

> volume #1.1.1.2 level 0.6527

> volume #1.1.1.2 level 0.4926

> volume #1.1.1.2 level 0.4855

> volume #1.1.1.2 level 0.4428

> volume #1.1.1.2 level 0.4179

> volume #1.1.1.2 level 0.4143

> clipper associate #2.2 toModel #1

Opened cryosparc_P120_J257_006_volume_map.mrc as #1.1.1.3, grid size
512,512,512, pixel 1.03, shown at step 1, values float32  

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

> volume #1.1.1.3 style surface

> volume #1.1.1.3 color #fffb3a

> volume #1.1.1.3 color #ff9131

> volume #1.1.1.3 level 0.2634

> volume #1.1.1.3 level 0.3978

> volume #1.1.1.3 level 0.2696

> volume #1.1.1.2 level 0.4535

> close #2.3

> volume #1.1.1.1 style mesh

> set bgColor white

> set bgColor black

> volume #1.1.1.1 level 0.4267

> volume #1.1.1.1 style surface

> volume #1.1.1.2 level 0.4321

> volume #1.1.1.2 style mesh

> volume #1.1.1.2 level 0.3813

> volume #1.1.1.2 style surface

> volume #1.1.1.1 level 0.3737

> volume #1.1.1.1 level 0.7154

> volume #1.1.1.1 level 0.4562

> volume #1.1.1.1 level 0.412

> volume #1.1.1.1 level 0.4091

> select ~sel & ##selected

1 atom, 1 residue, 1 model selected  

> select ~sel & ##selected

387691 atoms, 404232 bonds, 137 pseudobonds, 17924 residues, 4 models selected  

> select ~sel & ##selected

1 atom, 1 residue, 1 model selected  

> select ~sel & ##selected

387691 atoms, 404232 bonds, 137 pseudobonds, 17924 residues, 4 models selected  

> select ~sel & ##selected

1 atom, 1 residue, 1 model selected  

> volume #1.1.1.2 level 0.4273

> select /1

217 atoms, 221 bonds, 19 residues, 1 model selected  

> view sel

> clipper isolate /1 maskRadius 4.0 focus false

> volume #1.1.1.1 level 0.1992

Drag select of 1 residues  

> select clear

> volume #1.1.1.2 level 0.185

> volume #1.1.1.2 level 0.2522

> volume #1.1.1.2 level 0.2002

Drag select of 1 atoms, 1 residues, 2 bonds  
Drag select of 1 residues  

> close #1.1.1.1

> close #1.1.1.2

> close #1.1.1.3

> open
> /Users/julianaabramovich/Downloads/cryosparc_P120_J259_008_volume_map.mrc
> /Users/julianaabramovich/Downloads/cryosparc_P120_J262_009_volume_map.mrc
> /Users/julianaabramovich/Downloads/cryosparc_P120_J261_008_volume_map.mrc
> /Users/julianaabramovich/Downloads/cryosparc_P120_J260_007_volume_map.mrc

Opened cryosparc_P120_J259_008_volume_map.mrc as #3.1, grid size 512,512,512,
pixel 1.03, shown at level 0.197, step 2, values float32  
Opened cryosparc_P120_J262_009_volume_map.mrc as #3.2, grid size 512,512,512,
pixel 1.03, shown at level 0.204, step 2, values float32  
Opened cryosparc_P120_J261_008_volume_map.mrc as #3.3, grid size 512,512,512,
pixel 1.03, shown at level 0.199, step 2, values float32  
Opened cryosparc_P120_J260_007_volume_map.mrc as #3.4, grid size 512,512,512,
pixel 1.03, shown at level 0.201, step 2, values float32  

> clipper associate #3.1 toModel #1

Opened cryosparc_P120_J259_008_volume_map.mrc as #1.1.1.1, grid size
512,512,512, pixel 1.03, shown at step 1, values float32  

> volume #1.1.1.1 level 0.214

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

> volume #3.4 style mesh

> volume #3.4 level 0.4054

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

> volume #3.3 style mesh

> volume #3.3 level 0.3807

> select /w

318 atoms, 341 bonds, 10 residues, 1 model selected  

> view sel

> clipper isolate /w maskRadius 4.0 focus false

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

> volume #1.1.1.1 style surface

> clipper spotlight

> volume #1.1.1.1 level 0.3972

> volume #1.1.1.1 level 0.4349

> volume #1.1.1.1 level 0.3999

> clipper associate #3.2 toModel #1

Opened cryosparc_P120_J262_009_volume_map.mrc as #1.1.1.2, grid size
512,512,512, pixel 1.03, shown at step 1, values float32  

> volume #1.1.1.2 color #ff95eb

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

> volume #1.1.1.2 style surface

> volume #1.1.1.2 level 0.3469

> select clear

> volume #1.1.1.2 level 0.3946

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

> volume #1.1.1.2 level 0.3409

> volume #1.1.1.2 style mesh

> volume #1.1.1.2 level 0.3856

> volume #1.1.1.2 level 0.335

> volume #1.1.1.1 style mesh

> volume #1.1.1.1 level 0.3568

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

> volume #3.4 style surface

> volume #3.4 level 0.3396

Drag select of 1 residues  


===== 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 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

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: MacBookPro15,4
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
      OS Loader Version: 580.140.1~8

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 2 days, 23 hours, 7 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG 32 FHD:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55


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		Graphics		nonchimerax						all	ChimeraX