![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 18 months ago
Closed 18 months ago
#15168 closed defect (can't reproduce)
Crash changing Mac display configuration
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202405010532 (2024-05-01 05:32:45 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001d81cd000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, cython.cimports.libc.math, pyarrow.lib, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pyarrow._compute, pandas._libs.ops, numexpr.interpreter, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.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.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.atomic._ribbons, chimerax.graphics._graphics, PIL._imagingmath, chimerax.pdb._pdbio, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, 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.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 167)
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{
"uptime" : 410000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,4",
"coalitionID" : 12112,
"osVersion" : {
"train" : "macOS 14.2.1",
"build" : "23C71",
"releaseType" : "User"
},
"captureTime" : "2024-05-11 20:01:57.0157 +0200",
"codeSigningMonitor" : 1,
"incident" : "7908218D-B5B1-4C5A-A3C8-F9637392B971",
"pid" : 4464,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-06 16:30:36.2481 +0200",
"procStartAbsTime" : 3278167026147,
"procExitAbsTime" : 10041866370822,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"60406751-824C-51DE-863C-F25579392646","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4026A741-92F9-A7DA-403C-5C9CAE868976",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 17216,
"sleepWakeUUID" : "3C272F3D-40F1-4A81-BAF2-04D3E8E23500",
"sip" : "enabled",
"vmRegionInfo" : "0x59fed3e3b188 is not in any region. Bytes after previous region: 98469975142793 Bytes before following region: 6602104786552\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000059fed3e3b188","rawCodes":[1,98951011479944],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000059fed3e3b188"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":4464},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x59fed3e3b188 is not in any region. Bytes after previous region: 98469975142793 Bytes before following region: 6602104786552\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"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 =====
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
UCSF ChimeraX version: 1.8.dev202405010532 (2024-05-01)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/out_tracing/j007_run_TS019_data_righthanded_tr10.0nm.em
> format motl
> artiax clip off
Opened Particle list j007_run_TS019_data_righthanded_tr10.0nm.em with 5217
particles.
> artiax hide axes
5217 atoms, 5217 residues, atom cross_correlation range 0.0246 to 0.96
> artiax colormap #1.2.1.3 cross_correlation palette redgreen minValue
> 0.024582000449299812 maxValue 0.9603250026702881 transparency 0.0
> artiax particles #1.2.1 radius 6.64434524
5217 atoms, 5217 residues, atom cross_correlation range 0.0246 to 0.96
> artiax colormap #1.2.1.3 cross_correlation palette redgreen minValue
> 0.024582000449299812 maxValue 0.9603250026702881 transparency 0.0
5217 atoms, 5217 residues, atom legacy_x range -1 to 27
> artiax colormap #1.2.1.3 legacy_x palette redgreen minValue -1.0 maxValue
> 27.0 transparency 0.0
5217 atoms, 5217 residues, atom legacy_x range -1 to 27
> artiax colormap #1.2.1.3 legacy_x palette redgreen minValue -1.0 maxValue
> 27.0 transparency 0.0
> artiax particles #1.2.1 originScaleFactor 1.0
> artiax view xy
> artiax particles #1.2.1 originScaleFactor 1.0
> artiax view xy
Please enter a valid number for the pixelsize.
> artiax particles #1.2.1 originScaleFactor 3.942
> artiax view xy
> artiax view xz
> artiax view xy
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Inputs/j007_run_class001_righthand.mrc
Opened j007_run_class001_righthand.mrc as #2, grid size 64,64,64, pixel 3.94,
shown at level 0.609, step 1, values float32
> artiax attach #2 toParticleList #1.2.1
Opened j007_run_class001_righthand.mrc as #1.2.1.1.1, grid size 64,64,64,
pixel 3.94, shown at level 0.609, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 surfaceLevel 0.35953822
> combine #21
No structures specified
> lighting soft
> artiax particles #1.2.1 surfaceLevel 0.5373366
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters/motl_tomo19.0_cluster20.0.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster20.0.em with 20 particles.
> artiax particles #1.2.2 originScaleFactor 1.0
> artiax view xy
> artiax particles #1.2.2 originScaleFactor 3.942
> artiax view xy
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters/All_motl_tomo19.0_cluster20.0_entry.em
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters/All_motl_tomo19.0_cluster20.0_entry2.em
> format motl
> artiax clip off
Opened Particle list All_motl_tomo19.0_cluster20.0_entry.em with 20 particles.
Opened Particle list All_motl_tomo19.0_cluster20.0_entry2.em with 20
particles.
> artiax particles #1.2.3 originScaleFactor 3.942
> artiax view xy
> artiax particles #1.2.4 originScaleFactor 3.942
> artiax view xy
> artiax hide axes
> artiax particles #1.2.4 color 100,0,6,100
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/inputs/TS019_j007_run_data_righthand.em
> format motl
> artiax clip off
Opened Particle list TS019_j007_run_data_righthand.em with 5217 particles.
> artiax particles #1.2.5 originScaleFactor 3.942
> artiax view xy
> artiax hide axes
> hide #!1.2.4 models
> hide #!1.2.3 models
> hide #!1.2.2 models
> artiax hide surfaces
> artiax particles #1.2.5 radius 25.0875
> artiax particles #1.2.5 color 60,25,0,48
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/out_tracing/j007_run_TS019_data_righthanded_tr15.0nm.em
> format motl
> artiax clip off
Opened Particle list j007_run_TS019_data_righthanded_tr15.0nm.em with 5217
particles.
> artiax particles #1.2.6 originScaleFactor 1.0
> artiax view xy
> artiax particles #1.2.6 originScaleFactor 3.942
> artiax view xy
> artiax hide axes
> artiax particles #1.2.6 color 94,64,100,100
> artiax particles #1.2.6 color 94,64,100,77
> artiax particles #1.2.6 radius 20.32797619
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
5217 atoms, 5217 residues, atom cross_correlation range 0.0246 to 0.96
> artiax colormap #1.2.6.3 cross_correlation palette redgreen minValue
> 0.024582000449299812 maxValue 0.9603250026702881 transparency 22.61904762
5217 atoms, 5217 residues, atom legacy_x range -1 to 52
> artiax colormap #1.2.6.3 legacy_x palette redgreen minValue -1.0 maxValue
> 52.0 transparency 22.61904762
> hide #!1.2.6 models
> show #!1.2.6 models
> hide #!1.2.6 models
> show #!1.2.6 models
> hide #!1.2.6 models
> show #!1.2.6 models
> hide #!1.2.6 models
> show #!1.2.6 models
> show #!1.2.5 models
> hide #!1.2.5 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> show #!1.2.1 models
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters/All_motl_tomo19.0_cluster20.0_entry.em
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters/All_motl_tomo19.0_cluster20.0_entry2.em
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters/All_motl_tomo19.0_cluster20.0_exit.em
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters/All_motl_tomo19.0_cluster20.0_exit2.em
> format motl
> artiax clip off
Opened Particle list All_motl_tomo19.0_cluster20.0_entry.em with 20 particles.
Opened Particle list All_motl_tomo19.0_cluster20.0_entry2.em with 20
particles.
Opened Particle list All_motl_tomo19.0_cluster20.0_exit.em with 20 particles.
Opened Particle list All_motl_tomo19.0_cluster20.0_exit2.em with 20 particles.
> artiax particles #1.2.6 originScaleFactor 3.94
> artiax view xy
> artiax particles #1.2.4 originScaleFactor 3.94
> artiax view xy
> artiax particles #1.2.3 originScaleFactor 3.94
> artiax view xy
> artiax particles #1.2.2 originScaleFactor 3.04
> artiax view xy
> artiax particles #1.2.2 originScaleFactor 3.94
> artiax view xy
> hide #!1.2.5 models
> artiax view xy
> artiax hide markers
> artiax show markers
> artiax hide axes
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/A_linkers/motl_tomo19.0_cluster20.0_linkers.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster20.0_linkers.em with 10 particles.
> artiax particles #1.2.2 originScaleFactor 3.94
> artiax view xy
> artiax hide axes
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/templates/DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #2, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.2
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #1.2.2.1.1, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> artiax particles #1.2.2 surfaceLevel -0.49607564
> artiax hide axes
> artiax hide markers
> artiax show axes
> artiax hide axes
> artiax show surfaces
> artiax particles #1.2.2 surfaceLevel -0.19202928
> artiax particles #1.2.1 surfaceLevel 0.5847495
> x§
Unknown command: x§
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/A_linkers/motl_tomo19.0_cluster27.0_linkers.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster27.0_linkers.em with 13 particles.
> artiax particles #1.2.3 originScaleFactor 3.94
> artiax view xy
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/templates/DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #2, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.3
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #1.2.3.1.1, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> volume #1.2.3.1.1 capFaces false
> artiax show #1.2.3 surfaces
> artiax particles #1.2.3 surfaceLevel -0.17069269
> hide #!1.2.2 models
> artiax view xy
> artiax particles #1.2.3 surfaceLevel -0.25070489
> artiax particles #1.2.3 surfaceLevel -0.10134879
> artiax hide axes
> artiax hide markers
> artiax particles #1.2.1 surfaceLevel 0.56104305
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/A_linkers/motl_tomo19.0_cluster21.0_linkers.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster21.0_linkers.em with 10 particles.
> artiax particles #1.2.4 originScaleFactor 3.94
> artiax view xy
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/templates/DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #2, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.4
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #1.2.4.1.1, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> volume #1.2.4.1.1 capFaces false
> artiax show #1.2.4 surfaces
> artiax particles #1.2.4 surfaceLevel -0.52808052
> hide #!1.2.3 models
> artiax view xy
> artiax hide axes
> artiax hide markers
> artiax particles #1.2.4 surfaceLevel 0.0
> artiax particles #1.2.4 surfaceLevel -0.04267317
> artiax particles #1.2.4 transScaleFactor 1.0
> artiax view xy
> hide #!1.2.4 models
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/A_linkers/motl_tomo19.0_cluster11.0_linkers.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster11.0_linkers.em with 48 particles.
> artiax particles #1.2.5 originScaleFactor 3.94
> artiax view xy
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/templates/DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #2, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.5
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #1.2.5.1.1, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> volume #1.2.5.1.1 capFaces false
> artiax show #1.2.5 surfaces
> artiax particles #1.2.5 surfaceLevel -0.34138539
> artiax view xy
> artiax hide markers
> artiax hide axes
> artiax particles #1.2.5 surfaceLevel -0.13868781
> lighting full
> artiax particles #1.2.1 color 30,0,36,100
> artiax particles #1.2.1 color 0,46,86,100
> lighting soft
> set bgColor white
> graphics silhouettes true
> artiax particles #1.2.5 color 37,95,95,100
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/A_linkers/motl_tomo19.0_cluster7.0_linkers.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster7.0_linkers.em with 72 particles.
Please enter a valid number for the pixelsize.
> artiax particles #1.2.6 originScaleFactor 3.942
> artiax view xy
> hide #!1.2.5 models
> hide #!1.2.1 models
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters/motl_tomo19.0_cluster7.0.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster7.0.em with 234 particles.
> artiax particles #1.2.7 originScaleFactor 3.942
> artiax view xy
> artiax particles #1.2.7 color 0,46,86,100
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/inputs/j007_run_class001_righthand.mrc
Opened j007_run_class001_righthand.mrc as #2, grid size 64,64,64, pixel 3.94,
shown at level 0.609, step 1, values float32
> artiax attach #2 toParticleList #1.2.7
Opened j007_run_class001_righthand.mrc as #1.2.7.1.1, grid size 64,64,64,
pixel 3.94, shown at level 0.609, step 1, values float32
> volume #1.2.7.1.1 capFaces false
> artiax show #1.2.7 surfaces
> artiax hide axes
> artiax show surfaces
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/templates/DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #2, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.6
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #1.2.6.1.1, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> volume #1.2.6.1.1 capFaces false
> artiax show #1.2.6 surfaces
> artiax particles #1.2.6 surfaceLevel -0.50140979
> artiax hide markers
> artiax particles #1.2.6 surfaceLevel -0.1600244
> artiax particles #1.2.6 axesSize 59.13
> artiax particles #1.2.7 color 100,0,6,100
> artiax particles #1.2.7 color 37,95,95,100
> artiax particles #1.2.7 color 0,46,86,100
> artiax particles #1.2.7 color 94,64,100,100
> artiax particles #1.2.7 color 100,64,2,100
> artiax particles #1.2.7 color 0,46,86,100
> artiax particles #1.2.6 color 37,95,95,100
> artiax particles #1.2.6 color 0,46,86,100
> artiax particles #1.2.6 color 0,20,50,100
> artiax particles #1.2.6 color 100,0,6,100
> artiax particles #1.2.6 color 58,100,71,100
> artiax particles #1.2.6 color 37,95,95,100
> lighting soft
> lighting full
> lighting shadows false
> lighting simple
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
234 atoms, 234 residues, atom cross_correlation range 0.0377 to 0.813
> artiax colormap #1.2.7.3 cross_correlation palette redgreen minValue
> 0.03774699941277504 maxValue 0.8126090168952942 transparency 0.0
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters/motl_tomo19.0_cluster13.0.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster13.0.em with 110 particles.
> artiax particles #1.2.8 originScaleFactor 3.94
> artiax view xy
> hide #!1.2.7 models
> hide #!1.2.6 models
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/inputs/j007_run_class001_righthand.mrc
Opened j007_run_class001_righthand.mrc as #2, grid size 64,64,64, pixel 3.94,
shown at level 0.609, step 1, values float32
> artiax attach #2 toParticleList #1.2.8
Opened j007_run_class001_righthand.mrc as #1.2.8.1.1, grid size 64,64,64,
pixel 3.94, shown at level 0.609, step 1, values float32
> volume #1.2.8.1.1 capFaces false
> artiax show #1.2.8 surfaces
> artiax particles #1.2.8 color 0,46,86,100
> artiax particles #1.2.8 color 94,64,100,100
110 atoms, 110 residues, atom cross_correlation range 0.0462 to 0.634
> artiax colormap #1.2.8.3 cross_correlation palette redgreen minValue
> 0.046167001128196716 maxValue 0.6337329745292664 transparency 0.0
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/A_linkers/motl_tomo19.0_cluster13.0_linkers.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster13.0_linkers.em with 53 particles.
> artiax particles #1.2.9 originScaleFactor 3.94
> artiax view xy
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/templates/DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #2, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.9
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #1.2.9.1.1, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> volume #1.2.9.1.1 capFaces false
> artiax show #1.2.9 surfaces
> artiax particles #1.2.9 surfaceLevel -0.39472685
> artiax hide axes
> artiax view xy
> artiax hide markers
> artiax particles #1.2.9 surfaceLevel -0.03200488
> artiax particles #1.2.9 color 37,95,95,100
> lighting soft
> artiax particles #1.2.8 surfaceLevel 0.6163581
> artiax particles #1.2.8 color 37,95,95,100
> artiax particles #1.2.8 color 0,46,86,100
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters/motl_tomo19.0_cluster1.0.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster1.0.em with 829 particles.
> hide #!1.2.9 models
> hide #!1.2.8 models
> artiax particles #1.2.10 originScaleFactor 3.94
> artiax view xy
> show #!1.2.8 models
> show #!1.2.9 models
> save
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/chimeraSession_linkersTS019.cxs
> includeMaps true
> close session
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/bin4_voxel2.176_npc_whole.em
> format motl
/Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/bin4_voxel2.176_npc_whole.em
is likely not a motivelist.
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/bin4_voxel2.176_npc_whole.em
> format motl
/Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/bin4_voxel2.176_npc_whole.em
is likely not a motivelist.
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/CLEAN_TS_109_motl_ribosomes.em
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/CLEAN_TS_109_motl_vault.em
> format motl
> artiax clip off
Opened Particle list CLEAN_TS_109_motl_ribosomes.em with 643 particles.
Opened Particle list CLEAN_TS_109_motl_vault.em with 12 particles.
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/TS_109_NPC_ang5_CC0.1.star
> format star
rlnCoordinateZ was not found in any loop section of file
/Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/TS_109_NPC_ang5_CC0.1.star.
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/TS_109_motl_NPC_CC.0.02.em
> format motl
> artiax clip off
Opened Particle list TS_109_motl_NPC_CC.0.02.em with 5 particles.
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/bin4_voxel2.176_npc_whole.em
Opened bin4_voxel2.176_npc_whole.em as #2, grid size 240,240,240, pixel 1,
shown at level 5.3e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.3
Opened bin4_voxel2.176_npc_whole.em as #1.2.3.1.1, grid size 240,240,240,
pixel 1, shown at level 5.3e-05, step 1, values float32
> volume #1.2.3.1.1 capFaces false
> artiax show #1.2.3 surfaces
> artiax particles #1.2.3 surfaceLevel -0.15777701
> artiax particles #1.2.3 surfaceLevel -0.27768753
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/ROTmodel_vault_3.5res.em
Opened ROTmodel_vault_3.5res.em as #2, grid size 100,100,100, pixel 1, shown
at level 6.69e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.2
Opened ROTmodel_vault_3.5res.em as #1.2.2.1.1, grid size 100,100,100, pixel 1,
shown at level 6.69e-05, step 1, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> artiax particles #1.2.2 surfaceLevel -0.1736209
> artiax particles #1.2.2 color 76,0,53,100
> artiax particles #1.2.2 surfaceLevel -0.10653985
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/bin4_voxel2.176_ribosome.em
Opened bin4_voxel2.176_ribosome.em as #2, grid size 48,48,48, pixel 1, shown
at level 0.000569, step 1, values float32
> artiax attach #2 toParticleList #1.2.1
Opened bin4_voxel2.176_ribosome.em as #1.2.1.1.1, grid size 48,48,48, pixel 1,
shown at level 0.000569, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 surfaceLevel -0.00113396
> artiax particles #1.2.1 surfaceLevel -0.00097499
> artiax particles #1.2.1 color 17,81,28,100
> artiax hide axes
> artiax hide markers
> artiax view xy
> savepos
Unknown command: savepos
> savepos p1
Unknown command: savepos p1
> saveposition p1
Unknown command: saveposition p1
> save position p1
Cannot determine format for 'position'
> save pos p1
Cannot determine format for 'pos'
> save positions p1
Cannot determine format for 'positions'
> savepos p1
Unknown command: savepos p1
> view name p1
> ui tool show "Side View"
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> graphics silhouettes false
> view name p2
> fly p1 p2
> view
> select ~sel & ##selected
Nothing selected
> fly p1 p2
> view
> view orient
> ui tool show "Side View"
> rock
> rock 1,1,1
> rock 1,-1,1
> rock 1,-1,11
> rock 1,-1,-11
> stop
> view
> artiax view xy
> artiax clip toggle
No tomogram currently open.
> artiax clip toggle
No tomogram currently open.
> artiax clip toggle
No tomogram currently open.
> artiax clip toggle
No tomogram currently open.
> artiax clip toggle
No tomogram currently open.
> artiax clip toggle
No tomogram currently open.
> artiax clip toggle
No tomogram currently open.
> artiax clip toggle
No tomogram currently open.
> artiax clip toggle
No tomogram currently open.
> artiax view yz
> artiax clip toggle
No tomogram currently open.
> artiax view xz
> artiax view xy
> select clear
Drag select of surfaces, 4 of 643 instances
> select #1.2.1.2
1 model selected
> select #1.2.1.2
1 model selected
Drag select of surfaces, 1 of 639 instances
> artiax view xy
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/scores_membrane_clean.mrc
Opened scores_membrane_clean.mrc as #2, grid size 915,1331,335, pixel 1, shown
at step 1, values float32
> volume #2 region 0,0,0,914,1330,334 step 4
> volume #2 change image level 0,0 level 0.02785,0.8 level 0.2214,1
> volume #2 level 0.01166
> volume #2 level 0.0163
> volume #2 step 2
> volume #2 level 0.03635
> artiax view xy
> ui tool show "Side View"
> open "/Users/sergiocruz/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/9694974B-6FCA-4C76-9099-B07B3553721A/units_connected_min_nosol.pdb"
units_connected_min_nosol.pdb title:
MDANALYSIS FRAME 0: Created by PDBWriter [more info...]
Chain information for units_connected_min_nosol.pdb #3
---
Chain | Description
A | No description available
B | No description available
C G K O | No description available
D L | No description available
E M | No description available
F N | No description available
H P | No description available
I Q | No description available
J R | No description available
> hide #!1 models
> hide #!2 models
> view
> show #!2 models
> hide #3 models
> show #!1 models
> view
> artiax view xy
> rock 1,-1,1
> stop
> rock
> rock 1,1,1
> rock 1,1,1 20
> stop
> artiax view xy
> rock 1,1,1 90
> rock 1,1,1 90 100
> stop
> artiax view xy
> select add #2
3 models selected
> select add #2
3 models selected
> hide #!2 models
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> show #3 models
> show #!2 models
> select add #2
3 models selected
> select add #2
3 models selected
> hide #!2 models
> hide #!1 models
> select add #3
46971 atoms, 48857 bonds, 2222 residues, 4 models selected
> select add #2
46971 atoms, 48857 bonds, 2222 residues, 4 models selected
> select add #2
46971 atoms, 48857 bonds, 2222 residues, 4 models selected
> select add #2
46971 atoms, 48857 bonds, 2222 residues, 4 models selected
> select add #2
46971 atoms, 48857 bonds, 2222 residues, 4 models selected
> show #!2 models
> select add #2
46971 atoms, 48857 bonds, 2222 residues, 4 models selected
> select clear
> hide #!2 models
> view
> lighting soft
> graphics silhouettes true
> lighting soft
> roll
> stop
> color #3 bychain
> show #3 cartoons
> hide #3 cartoons
> hide #3 atoms
> show #3 cartoons
> roll
> stop
> hide #!1.2.3 models
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters_19nm/motl_tomo19.0_cluster73.0.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster73.0.em with 80 particles.
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #3 models
> hide #!1.2.2 models
> hide #!1.2.1 models
> artiax particles #1.2.4 originScaleFactor 3.94
> artiax view xy
> hide #1.2.4.3 cartoons
> artiax hide axes
> artiax particles #1.2.4 originScaleFactor 3.942
> artiax view xy
> artiax attach #2 toParticleList #1.2.4
Opened scores_membrane_clean.mrc as #1.2.4.1.1, grid size 915,1331,335, pixel
1, shown at level 0.0185, step 2, values float32
> volume #1.2.4.1.1 capFaces false
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/templates/DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #2, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.4
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #1.2.4.1.1, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> volume #1.2.4.1.1 capFaces false
> artiax show #1.2.4 surfaces
> artiax particles #1.2.4 surfaceLevel -0.02192383
> artiax hide markers
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/A_linkers_19nm/motl_tomo19.0_cluster73.0_linkers.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster73.0_linkers.em with 41 particles.
> artiax particles #1.2.5 originScaleFactor 3.942
> artiax view xy
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/inputs/j007_run_class001_righthand.mrc
Opened j007_run_class001_righthand.mrc as #2, grid size 64,64,64, pixel 3.94,
shown at level 0.609, step 1, values float32
> artiax attach #2 toParticleList #1.2.5
Opened j007_run_class001_righthand.mrc as #1.2.5.1.1, grid size 64,64,64,
pixel 3.94, shown at level 0.609, step 1, values float32
> volume #1.2.5.1.1 capFaces false
> artiax show #1.2.5 surfaces
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/templates/DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #2, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.5
Opened DNA_bin1_1.971voxel_52bp_molmap_3.5_inv.mrc as #1.2.5.1.1, grid size
101,101,101, pixel 1.97, shown at level 8.96e-05, step 1, values float32
> volume #1.2.5.1.1 capFaces false
> artiax show #1.2.5 surfaces
> artiax particles #1.2.5 surfaceLevel -0.00548096
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/A_linkers_19nm/motl_tomo19.0_cluster73.0_linkers.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster73.0_linkers.em with 41 particles.
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/outputs/clusters_19nm/motl_tomo19.0_cluster73.0.em
> format motl
> artiax clip off
Opened Particle list motl_tomo19.0_cluster73.0.em with 80 particles.
> artiax particles #1.2.4 originScaleFactor 3.942
> artiax view xy
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/git_repo/linker_prediction/Notebook/Nova_interpol_TM_019/inputs/j007_run_class001_righthand.mrc
Opened j007_run_class001_righthand.mrc as #2, grid size 64,64,64, pixel 3.94,
shown at level 0.609, step 1, values float32
> artiax attach #2 toParticleList #1.2.4
Opened j007_run_class001_righthand.mrc as #1.2.4.1.1, grid size 64,64,64,
pixel 3.94, shown at level 0.609, step 1, values float32
> volume #1.2.4.1.1 capFaces false
> artiax show #1.2.4 surfaces
> artiax particles #1.2.4 surfaceLevel 0.58268334
> artiax hide axes
> artiax hide markers
80 atoms, 80 residues, atom cross_correlation range 0.0629 to 0.629
> artiax colormap #1.2.4.3 cross_correlation palette redgreen minValue
> 0.06285399943590164 maxValue 0.6285669803619385 transparency 0.0
> artiax particles #1.2.5 color 76,0,53,100
> artiax particles #1.2.5 color 37,95,95,100
> roll
> artiax particles #1.2.4 surfaceLevel 0.38375214
> artiax particles #1.2.4 surfaceLevel 0.41623071
> set bgColor white
> video record
Unknown command: video record
> movie record
> movie encode
Movie saved to /Users/sergiocruz/Desktop/movie.mp4
> stop
> roll
> stop
> hide #!1.2.5 models
> show #3 models
> hide #!1 models
> view
> hide #3 models
> show #3 models
> show #!1 models
> hide #3 models
> view
> roll
> stop
> show #3 models
> hide #!1 models
> view orient
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/Notebooks/output2/motl_tomo19.0_cluster13.0.em
> artiax clip off
Opened Particle list motl_tomo19.0_cluster13.0.em with 13 particles.
> artiax particles #1.2.6 originScaleFactor 1.97
> artiax view xy
> artiax particles #1.2.6 radius 19.17173145
> view orient
> view
> view orient
> hide #!1.2.4 models
> view
> artiax particles #1.2.6 radius 19.17173145
> artiax particles #1.2.6 radius 21.99717314
> show #!1 models
> view
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/T-cells/Resting/Nucleosome_classification/j043_Refine3D/j045_postprocess_masked_righthand.mrc
Opened j045_postprocess_masked_righthand.mrc as #2, grid size 140,140,140,
pixel 1.97, shown at level 0.558, step 1, values float32
> artiax attach #2 toParticleList #1.2.6
Opened j045_postprocess_masked_righthand.mrc as #1.2.6.1.1, grid size
140,140,140, pixel 1.97, shown at level 0.558, step 1, values float32
> volume #1.2.6.1.1 capFaces false
> artiax show #1.2.6 surfaces
> artiax particles #1.2.6 surfaceLevel 1.01111669
> view
Drag select of axes, surfaces, 13 atoms
> ui mousemode right "translate picked particle"
> ui mousemode right "translate selected particles"
> artiax view xy
> artiax particles #1.2.6 surfaceLevel 0.87023421
> select clear
> artiax particles #1.2.6 surfaceLevel 0.63878443
> artiax particles #1.2.6 color 94,64,100,67
> artiax hide axes
> artiax hide markers
Drag select of surfaces, 3 of 13 instances
> ui mousemode right "delete picked particle"
> select clear
Drag select of surfaces, 1 of 10 instances, 3 residues
> select clear
Drag select of surfaces, 1 of 9 instances
Drag select of surfaces, 3 of 8 instances
> hide #3 models
Drag select of surfaces
> show #3 models
> undo
> show #3 models
> undo
Undo failed, probably because structures have been modified.
> show #3 models
> show #3 surfaces
> lighting soft
> color #3.1 #0433ffff
> color #3.2 #8efa00ff
> color #3.2 #00fdffff
> color #3.2 #0096ffff
> color #3.2 white
> color #3.1 #7a81ffff
> color #3.1 #0433ffff
> color #3.1 #011993ff
> color #3.1 #0096ffff
> color #3.1 #0096ffc8
> color #3.1 #0096ffd2
> color #3.2 #ffffff80
> color #3.1 #0096ff7c
> show #!3 atoms
> hide #3.1 models
> show #3.1 models
> color #3.10 #00fa92ff
> color #3.10 #9437ffff
> hide #!3 models
> show #!3 models
> show #!1.2.3 models
> hide #!1.2.3 models
> show #!1.2.3 models
> hide #!1.2.3 models
> show #!1.2.3 models
> hide #!1.2.3 models
> show #!1.2.3 models
> show #!1.2.2 models
> show #!1.2.1 models
> show #!1.2.5 models
> hide #!1.2.5 models
> hide #!3 models
> hide #!1.2.3 models
> show #!1.2.3 models
> hide #!1.2.3 models
> hide #!1.2.2 models
> hide #!1.2.1 models
> show #!1.2.1 models
> show #!1.2.2 models
> show #!1.2.3 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!3 models
> hide #!3 models
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/scores_membrane_clean.mrc
Opened scores_membrane_clean.mrc as #2, grid size 915,1331,335, pixel 1, shown
at step 1, values float32
> volume #1.2.4.1.1 level 0.3808
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #2 region 0,0,0,914,1330,334 step 4
> view orient
> surface dust #2 size 10
> volume #2 color #ff40ff
> volume #2 color #ff85ff
> volume #2 color #eeeeec
> volume #2 color #ff85ff
> volume #2 color #ff5dee
> artiax particles #1.2.3 color 50,50,50,100
> artiax particles #1.2.3 color 84,84,84,100
> artiax particles #1.2.3 color 92,92,92,100
> artiax particles #1.2.3 color 100,100,100,100
> artiax particles #1.2.3 surfaceLevel -0.04870459
> artiax view xy
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #2 step 1
> volume #2 level 0.029
> volume #!2 showOutlineBox true
> set bgColor black
> set bgColor transparent
> lighting soft
> lighting full
> set bgColor black
> lighting simple
> lighting soft
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> artiax particles #1.2.1 color 17,81,28,100
> artiax particles #1.2.1 color 45,98,47,100
> artiax particles #1.2.1 color 0,98,0,100
> artiax particles #1.2.1 surfaceLevel -0.00085671
> surface dust #2 size 10
> save
> /Users/sergiocruz/Desktop/VisualProteomics/Papers/ArtiaX/ArtiaX_TS_109.cxs
> includeMaps true
> hide #!1.2.3 models
> hide #!1.2.2 models
> hide #!1.2.1 models
> ui tool show "Map Eraser"
> volume erase #2 center 517.6,79.906,200.17 radius 98.973
Opened scores_membrane_clean.mrc copy as #5, grid size 915,1331,335, pixel 1,
shown at step 1, values float32
> volume erase #5 center 665.77,400.95,97.495 radius 98.494
> volume erase #5 center 529.91,570.18,90.053 radius 98.494
> volume erase #5 center 504.03,620.72,56.249 radius 98.494
> volume erase #5 center 492.91,623.64,123.06 radius 98.494
> volume erase #5 center 128.93,647.6,342.75 radius 98.494
> volume erase #5 center 699.43,56.338,376.4 radius 98.494
> volume erase #5 center 616.83,46.792,253.83 radius 98.494
> volume erase #5 center 935.93,-56.711,260.52 radius 98.494
> volume erase #5 center 1022.5,-36.685,158.29 radius 98.494
> volume erase #5 center 970.33,48.788,82.89 radius 98.494
> volume erase #5 center 918.48,418.34,405.43 radius 98.494
> volume erase #5 center 153.33,407.37,117.04 radius 63.223
> volume erase #5 center 137.66,417.3,87.5 radius 63.223
> volume erase #5 center 188.85,640.79,74.961 radius 63.223
> volume erase #5 center 220.09,679.54,125.15 radius 63.223
> volume erase #5 center 159.8,983.1,103.44 radius 63.223
> volume erase #5 center 130.31,1009.4,84.054 radius 63.223
> volume erase #5 center 214.54,916.58,143.95 radius 63.223
> volume erase #5 center 652.12,522.25,393.12 radius 63.223
> volume erase #5 center 599.33,183.2,347.69 radius 63.223
> volume erase #5 center 801.21,103.13,372.53 radius 63.223
> volume erase #5 center 801.21,103.13,372.53 radius 187.01
> volume erase #5 center 909.93,161.37,204.69 radius 187.01
> volume #5 level 0.03251
> surface dust #5 size 10
> show #!1.2.1 models
> show #!1.2.2 models
> show #!1.2.3 models
> artiax particles #1.2.1 surfaceLevel -0.00107241
> volume #!5 showOutlineBox false
> movie record
> rock 1,1,0 20
> wait 20
> rock 1,1,0 20
> stop
> movie encode
Movie saved to /Users/sergiocruz/Desktop/movie.mp4
> volume #!5 showOutlineBox true
> volume #!5 showOutlineBox false
> save
> /Users/sergiocruz/Desktop/VisualProteomics/Papers/ArtiaX/ArtiaX_TS_109.cxs
> includeMaps true
> movie record
> rock 1,1,0 20
> stop
> movie encode
Movie saved to /Users/sergiocruz/Desktop/movie.mp4
> hide #!1.2.3 models
> show #!1.2.3 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!5 models
> show #!5 models
> view name p1
> hide #!1.2 models
> hide #!5 models
> view name p2
> show #!1.2.3 models
> show #!1.2.1 models
> show #!1.2.2 models
> show #!5 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> ui mousemode right "mark point"
> show #!1.2.2 models
> hide #!1.2.2 models
> marker #1.2.2.3 position 57.31,1038,270.1 color #c20088 radius 4
> marker #1.2.2.3 position 57.13,1039,270.1 color #c20088 radius 4
> ui mousemode right "mark point"
> marker #1.2.2.3 position 56.59,1037,270 color #c20088 radius 4
> hide #!1.2.1 models
> show #!1.2.1 models
> artiax clip toggle
No tomogram currently open.
> artiax clip toggle
No tomogram currently open.
> marker #1.2.1.3 position 36.26,1038,269.8 color #00f900 radius 4
> artiax view xy
> artiax view xz
> artiax view yz
> artiax view xy
> hide #!1.2.3 models
> show #!1.2.3 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> select clear
Drag select of surfaces, 1 of 639 instances
Drag select of surfaces, 1 of 639 instances, surfaces, 3 of 15 instances
> show #!1.2.5 models
> artiax hide surfaces
> artiax show markers
> marker #7 position 57,1045, 215
> hide #!1.2.5 models
> hide #!1.2.3 models
> hide #!1.2.2 models
> hide #!1.2.1 models
> show #!1.2.2 models
> show #!1.2.1 models
> show #!1.2.3 models
> show all
> artiax show surfaces
> view name p3
> zoom 1.25
> turn x 90
> turn x -90
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> turn y -90
> turn y 90
> turn z 90
> turn z -90
> turn x -90
> zoom 2
> zoom .5
> zoom 3
> move x -30
> move x 30
> zoom .33333333
> view name p4
> zoom 4
> move x -10
> move x 10
> lighting flat
> lighting full
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting full
> lighting shadows false
> lighting soft
> artiax particles #1.2.2 surfaceLevel -0.0046843
> artiax particles #1.2.2 surfaceLevel -0.73084954
> artiax particles #1.2.2 surfaceLevel -0.0046843
> artiax particles #1.2.1 surfaceLevel -0.00088367
> artiax hide markers
> view name p5
> save
> /Users/sergiocruz/Desktop/VisualProteomics/Papers/ArtiaX/ArtiaX_TS_109_1.cxs
> movie record
> fly p1 p2
> crossface; hide all
Unknown command: crossface; hide all
> crossfade
> hide all
> roll y 4 90 center #7
> show #!1.2.2 models
> show #!1.2 models
> fly p2 60 p3 60 p4 p5 p7
fly: Unknown position name "p7"
> fly p2 60 p3 60 p4 p5
> show #!2 models
> hide #!2 models
> artiax show surfaces
> artiax show markers
> artiax show axes
> artiax show surfaces
> movie encode
Movie saved to /Users/sergiocruz/Desktop/movie.mp4
> artiax view xy
> crossfade
> show all
> fly p1 p2
> artiax hide axes
> view name pp1
> turn x -90
> zoom 5
> move x 50
> view name pp2
> fly pp1 pp2
> ahow pp1
Unknown command: ahow pp1
> show pp1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> view pp1
> fly pp1 pp2 100
> zoom 5
> view pp1
> fly pp1 pp2 100
> zoom 5 40
> volume #5 level 0.05913
> fly pp2 pp1 100
> zoom .25 40
> fly pp1 pp2 100
> zoom 5 40
> fly pp1 pp2 100
> zoom 0.25
> zoom 5 40
> fly pp2 pp1 100
> zoom 0.25
> zoom .25 40
> view p1
> fly pp1 pp2 100
> zoom 0.25
> view p1
> fly pp1 pp2 100
> zoom 5
> view p1
> fly pp1 pp2 100
> zoom 5 40
> view p1
> fly pp1 pp2 100
> zoom 5 100
> fly pp2 pp1 100
> zoom .255 100
> view p1 100
> crossfade
> hide #!1.2.1 models
> hide #!1.2.2 models
> hide #!1.2.3 models
> view p1 100
> crossfade
> hide #!1.2.1 models
> hide #!1.2.2 models
> hide #!1.2.3 models
> crossfade hide #!1.2.1 models; hide #!1.2.2 models; hide #!1.2.3 models;
Expected an integer >= 1 or a keyword
> crossfade 10 hide #!1.2.1 models; hide #!1.2.2 models; hide #!1.2.3 models;
Expected a keyword
> crossfade
> hide #!1.2.1 models
> hide #!1.2.2 models
> hide #!1.2.3 models
> show #!1.2.1 models 20
Expected ',' or a keyword
> show #!1.2.1 models, 20
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> view pp1 20
> show #!1.2.1 models
> view pp1 20
> show #!1.2.2 models
> view pp1 20
> show #!1.2.3 models
> view pp1 50
> hide %3 models
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> view pp1 50
> hide #!5 models
> view pp1 50
> show #!5 models
> open
> /Users/sergiocruz/Desktop/VisualProteomics/Papers/ArtiaX/TS_126/templates/model_vault_3.5res.em
Opened model_vault_3.5res.em as #4, grid size 100,100,100, pixel 1, shown at
level 6.63e-05, step 1, values float32
> hide #!1.2.3 models
> hide #!1.2.2 models
> hide #!1.2.1 models
> view
> hide #7 models
> view
> select add #4
2 models selected
> hide #!4 models
> select subtract #4
Nothing selected
> volume #4 level -0.2853
> view
> volume capFaces true
> volume capFaces false
> volume #4 level -0.04034
> ui tool show "Map Eraser"
> view
> volume erase #4 center 49.63,50.143,64.072 radius 34.863
Opened model_vault_3.5res.em copy as #8, grid size 100,100,100, pixel 1, shown
at step 1, values float32
> undo
> show #!4 models
> view
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #4.1 models
> show #4.1 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #4.1 models
> hide #!4 models
> show #!4 models
> show #!8 models
> close #8
> hide #!4 models
> show #!4 models
> show #4.1 models
> ui tool show "Map Eraser"
> volume erase #4 center 47.307,50.797,64.698 radius 31.033
Opened model_vault_3.5res.em copy as #8, grid size 100,100,100, pixel 1, 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.
> save
> /Users/sergiocruz/Desktop/VisualProteomics/Papers/ArtiaX/TS_126/templates/OPEN_bin4_vault.mrc
> models #8
> close #8
> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/all_macromolecules/TS_109/CLEAN_TS_109_motl_vault.em
> format motl
> artiax clip off
Opened Particle list CLEAN_TS_109_motl_vault.em with 12 particles.
> view
> artiax attach #2 toParticleList #1.2.6
Opened scores_membrane_clean.mrc as #1.2.6.1.1, grid size 915,1331,335, pixel
1, shown at level 0.0185, step 1, values float32
> volume #1.2.6.1.1 capFaces false
> open
> /Users/sergiocruz/Desktop/VisualProteomics/Papers/ArtiaX/TS_126/templates/OPEN_bin4_vault.mrc
Opened OPEN_bin4_vault.mrc as #2, grid size 100,100,100, pixel 1, shown at
level 6.63e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.6
Opened OPEN_bin4_vault.mrc as #1.2.6.1.1, grid size 100,100,100, pixel 1,
shown at level 6.63e-05, step 1, values float32
> volume #1.2.6.1.1 capFaces false
> artiax show #1.2.6 surfaces
> artiax particles #1.2.6 surfaceLevel -0.0
> show #!1.2.1 models
> show #!1.2.2 models
> show #!1.2.3 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.5 models
> hide #!1.2.5 models
> view
> hide #!1.2.1 models
> hide #!1.2.3 models
> hide #!1.2.2 models
Drag select of axes, 1 of 12 instances, surfaces, 1 of 12 instances, 1 atoms
> ui mousemode right "rotate selected particles"
> show #!1.2.2 models
> select clear
> hide #!1.2.2 models
> show #!1.2.1 models
> artiax hide axes
> artiax hide markers
> show #!1.2.2 models
> hide #!1.2.2 models
===== Log before crash end =====
Log:
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
UCSF ChimeraX version: 1.8.dev202405010532 (2024-05-01)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
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: MacBookPro18,4
Model Number: Z15G002NZD/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 7 days, 12 hours, 58 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
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: No
Connection Type: Internal
DELL U2715H:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
annotated-types: 0.6.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
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: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.4.7
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.4
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.3
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-ColorActions: 1.0.4
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202405010532
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
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
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
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
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: 1.0.3
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: 1.16.3
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: 1.38
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
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: 1.1.3
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: 4.51.0
funcparserlib: 2.0.0a0
geomdl: 5.3.1
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: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
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
pandas: 2.2.2
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: 4.2.1
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pyarrow: 16.0.0
pycollada: 0.8
pydantic: 2.7.1
pydantic-core: 2.18.2
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: 26.0.2
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
starfile: 0.5.7
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 18 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash changing display configuration |
comment:2 by , 18 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash changing display configuration → Crash changing Mac display configuration |
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Qt bug with multiple displays on Mac.
Maybe the user plugged in or unplugged a monitor, the Qt crashed. They were using the built-in MacBook Pro display and a DELL U2715H external display when they submitted the bug report.
4 stack frame calls from deepest to less deep: