![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 22 months ago
Closed 17 months ago
#10387 closed defect (fixed)
Crash in garbage collection saving session
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.4-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x0000000117a95600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2000 in save_state
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 219 in take_snapshot
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1417 in take_snapshot
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 296 in process
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 273 in discovery
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 636 in save
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 912 in save
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.dssp._dssp, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, 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.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, 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.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.__nnls, 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.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 119)
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{
"uptime" : 170000,
"procLaunch" : "2023-12-20 14:57:45.7716 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,3",
"procStartAbsTime" : 133135645954908,
"coalitionID" : 15139,
"osVersion" : {
"train" : "macOS 12.4",
"build" : "21F79",
"releaseType" : "User"
},
"captureTime" : "2023-12-21 14:57:03.0824 +0100",
"incident" : "14F6C776-8A41-4A24-8F43-03412F01DC5C",
"bug_type" : "309",
"pid" : 32870,
"procExitAbsTime" : 170939645496900,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D77DF969-7497-5E85-83B5-874A6142407E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1A6806F6-AE08-11C2-BA1A-F633BED1665C",
"wakeTime" : 25618,
"bridgeVersion" : {"build":"19P5071","train":"6.5"},
"sleepWakeUUID" : "B17C9B5B-0741-4589-B574-E45874D145F3",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487556439\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff3d000-7ffffff3e000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487556439\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff3d000-7ffffff3e000 [ 4K] r-x\/r-x SM=ALI ",
"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 =====
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/mS22.cxs
> format session
opened ChimeraX session
Chains must have same sequence
> info selection level residue
residue id #1.8/AD:369 name HIS index 281
> ui tool show "Show Sequence Viewer"
> sequence chain #1.8/AD
Chains must have same sequence
> select #1.22/AR:114
10 atoms, 9 bonds, 1 residue, 1 model selected
Alignment identifier is 1.22/AR
> select #1.8/AD:370
16 atoms, 15 bonds, 1 residue, 1 model selected
Chains must have same sequence
> select #1.8/AD:362
19 atoms, 18 bonds, 1 residue, 1 model selected
Chains must have same sequence
> select #1.22/AR:104
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide #!5 models
> show #!5 models
> select add #5.18/Ca:357
28 atoms, 26 bonds, 2 residues, 2 models selected
Destroying pre-existing alignment with identifier 1.22/AR
Alignment identifier is 1.22/AR
Alignment identifier is 5.18/Ca
> select #1.22/AR:101
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.22/AR:101
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #5.18/Ca:354
21 atoms, 20 bonds, 2 residues, 2 models selected
> select sequence PYRFLQTE
74 atoms, 76 bonds, 8 residues, 1 model selected
> select #1.22/AR:101
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.22/AR:101
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.22/AR:101-102
28 atoms, 28 bonds, 2 residues, 1 model selected
> select #1.22/AR:101-105
90 atoms, 91 bonds, 5 residues, 1 model selected
> hide #!5 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> select clear
> ui tool show "Side View"
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_22_Hs.png
> width 3000 height 2182 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_22_Sc.png
> width 3000 height 2182 supersample 3 transparentBackground true
> show #!3 models
> hide #!2 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_22_At.png
> width 3000 height 2182 supersample 3 transparentBackground true
> view name 5_22
> show #!5 models
> hide #!3 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_22_Tb.png
> width 3000 height 2182 supersample 3 transparentBackground true
> view 5_22
> show #!6 models
> hide #!5 models
> show #!4 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view 5_22
> hide #!4 models
> show #!4 models
> hide #!1 models
> ~ribbon #4.41
> view 5_22
> show #!1 models
> hide #!1 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_22_Tt.png
> width 3000 height 2182 supersample 3 transparentBackground true
> view default
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/mS22.cxs
> ribbon #4.41
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
Drag select of 135 residues
> dssp sel
> dssp sel energyCutoff -0.1
> hide #!3 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> view name S16_22
> show #!1 models
> hide #!5 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S16_22_Hs.png
> width 3000 height 2182 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S16_22_Sc.png
> width 3000 height 2182 supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> select clear
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_16_At.png
> width 3000 height 2182 supersample 3 transparentBackground true
> hide #!3 models
> show #!4 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S16_22_Tt.png
> width 3000 height 2182 supersample 3 transparentBackground true
> hide #!4 models
> show #!5 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S16_22_Tb.png
> width 3000 height 2182 supersample 3 transparentBackground true
> view default
> show #!1 models
> hide #!5 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> view S5_22
Expected an objects specifier or a view name or a keyword
> view 5_22
> view default
> hide #!3 models
> show #!4 models
> show #!6 models
> hide #!4 models
> view default
> surface #6
> ~surface #6.5,16
> silhouette afda
Unknown command: silhouette afda
> sillhouete afda
Unknown command: sillhouete afda
> silhouettes fads
Unknown command: silhouettes fads
> silhouette fads
Unknown command: silhouette fads
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting soft
> graphics silhouettes width 1
> graphics silhouettes width 2
> graphics silhouettes width 3
> graphics silhouettes width 2
> graphics silhouettes width 3
> graphics silhouettes
Current silhouette settings:
enabled: True
width: 3
color: 0,0,0
depth jump: 0.03
> graphics silhouettes
Current silhouette settings:
enabled: True
width: 3
color: 0,0,0
depth jump: 0.03
> graphics silhouettes width 2
> graphics silhouettes width 2 depthJump 0.1
> graphics silhouettes width 2 depthJump 0.06
> view default
> graphics silhouettes width 2 depthJump 0.03
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_16_22_silhouetteEc.png
> width 3000 height 2182 supersample 3 transparentBackground true
> close session
> open "/Users/ondrejgahura/Work/Lab
> Book/Mitoribosomes/_LECA_mitoribosome/Structure_analyses/mtSSU_start.cxs"
> format session
opened ChimeraX session
> hide #!10 models
> hide #!11 models
> select add #6.13
909 atoms, 900 bonds, 133 residues, 1 model selected
> show #!1 models
> ribbon #1
> show #!2 models
> hide #!2 models
> ribbon #1-6
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select add #6.19
1601 atoms, 1585 bonds, 241 residues, 2 models selected
> show #!5 models
> close #7-11
> close #2,4
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/uS13m.cxs
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #!5 models
> color dimgrey
> hide #!5 models
> hide #!3 models
> hide #!1 models
> color name c4 #FC7300
Color 'c4' is opaque: rgb(98.8%, 45.1%, 0%) hex: #fc7300
> color #6.13#3.29
> color #6.13#3.29 c4
> select clear
> lighting simple
> lighting soft
> show #!1 models
> hide #!6 models
> select #1.5/AA:5080
18 atoms, 19 bonds, 1 residue, 1 model selected
> select add #1.5/AA:5087
39 atoms, 42 bonds, 2 residues, 1 model selected
> select add #1.10/AF:311
60 atoms, 65 bonds, 3 residues, 2 models selected
> select add #1.10/AF:320
81 atoms, 88 bonds, 4 residues, 2 models selected
> select add #1.10/AF:305
102 atoms, 111 bonds, 5 residues, 2 models selected
> select add #1.10/AF:301
123 atoms, 134 bonds, 6 residues, 2 models selected
Alignment identifier is 1.5/AA
Chains must have same sequence
> select #1.5/AA:5047
18 atoms, 19 bonds, 1 residue, 1 model selected
> select #1.5/AA:5047-5078,5080-5087
772 atoms, 865 bonds, 40 residues, 1 model selected
> ~ribbon sel
> select #1.10/AF:311
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #1.10/AF:170
37 atoms, 38 bonds, 2 residues, 1 model selected
> select add #1.10/AF:301
58 atoms, 61 bonds, 3 residues, 1 model selected
> select add #1.10/AF:319
76 atoms, 80 bonds, 4 residues, 1 model selected
Chains must have same sequence
Chains must have same sequence
> select add #1.10/AF:312
97 atoms, 103 bonds, 5 residues, 1 model selected
> select add #1.10/AF:313
119 atoms, 127 bonds, 6 residues, 1 model selected
> select add #1.10/AF:314
140 atoms, 150 bonds, 7 residues, 1 model selected
> select add #1.10/AF:303
158 atoms, 169 bonds, 8 residues, 1 model selected
> select subtract #1.10/AF:303
140 atoms, 150 bonds, 7 residues, 1 model selected
> select add #1.10/AF:302
161 atoms, 173 bonds, 8 residues, 1 model selected
> select add #1.10/AF:303
179 atoms, 192 bonds, 9 residues, 1 model selected
> select add #1.10/AF:304
200 atoms, 215 bonds, 10 residues, 1 model selected
> select add #1.10/AF:305
221 atoms, 238 bonds, 11 residues, 1 model selected
> select subtract #1.10/AF:170
205 atoms, 223 bonds, 10 residues, 1 model selected
> select add #1.10/AF:317
223 atoms, 242 bonds, 11 residues, 1 model selected
> select add #1.10/AF:316
241 atoms, 261 bonds, 12 residues, 1 model selected
> select add #1.10/AF:318
259 atoms, 280 bonds, 13 residues, 1 model selected
> select add #1.10/AF:315
277 atoms, 299 bonds, 14 residues, 1 model selected
> select add #1.10/AF:320
298 atoms, 322 bonds, 15 residues, 1 model selected
> delete sel
> select #1.10/AF:306
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #1.10/AF:310
39 atoms, 42 bonds, 2 residues, 1 model selected
> select add #1.10/AF:309
57 atoms, 61 bonds, 3 residues, 1 model selected
> select add #1.10/AF:308
78 atoms, 84 bonds, 4 residues, 1 model selected
> select add #1.10/AF:307
99 atoms, 107 bonds, 5 residues, 1 model selected
> delete sel
> show #!5 models
> hide #!5 models
> show #!6 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/uS13m.cxs
> show #!5 models
> hide #!1 models
> select #5.54/DX:52
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
291 atoms, 298 bonds, 34 residues, 1 model selected
> select up
1196 atoms, 1231 bonds, 141 residues, 1 model selected
> select down
291 atoms, 298 bonds, 34 residues, 1 model selected
> select up
1196 atoms, 1231 bonds, 141 residues, 1 model selected
> select down
291 atoms, 298 bonds, 34 residues, 1 model selected
> select up
1196 atoms, 1231 bonds, 141 residues, 1 model selected
> select up
177122 atoms, 182802 bonds, 20809 residues, 63 models selected
> select down
1196 atoms, 1231 bonds, 141 residues, 1 model selected
> select up
177122 atoms, 182802 bonds, 20809 residues, 63 models selected
> select down
1196 atoms, 1231 bonds, 141 residues, 1 model selected
> color name c2 #1F8A70
Color 'c2' is opaque: rgb(12.2%, 54.1%, 43.9%) hex: #1f8a70
> color name c3 #BFDB38
Color 'c3' is opaque: rgb(74.9%, 85.9%, 22%) hex: #bfdb38
> color name c1 #00425A
Color 'c1' is opaque: rgb(0%, 25.9%, 35.3%) hex: #00425a
> color sel c2
> select #5.32/DB:1151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
30 atoms, 31 bonds, 3 residues, 1 model selected
> select up
9148 atoms, 9369 bonds, 1111 residues, 1 model selected
> color sel c3
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select clear
> select add #1
120930 atoms, 124301 bonds, 913 pseudobonds, 6512 residues, 44 models selected
> show sel atoms
> hide sel atoms
> color sel white
> select clear
> select #6.13/M:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
139 atoms, 138 bonds, 18 residues, 1 model selected
> select up
891 atoms, 900 bonds, 115 residues, 1 model selected
> surface sel
> transparency sel 80 surfaces
> select clear
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #5
177122 atoms, 182802 bonds, 293 pseudobonds, 20809 residues, 91 models
selected
> select subtract #5/DB,DX
166778 atoms, 172202 bonds, 293 pseudobonds, 19557 residues, 89 models
selected
> color sel white
> hide #!1 models
> show #!1 models
> cartoon style xsection barbell barSides 18 barScale 0.4 thickness 0.8 width
> 3
> select clear
> lighting soft
> lighting simple
> color name p2_1 #557B83
Color 'p2_1' is opaque: rgb(33.3%, 48.2%, 51.4%) hex: #557b83
> color name p2_2 #39AEA9
Color 'p2_2' is opaque: rgb(22.4%, 68.2%, 66.3%) hex: #39aea9
> color name p2_3 #A2D5AB
Color 'p2_3' is opaque: rgb(63.5%, 83.5%, 67.1%) hex: #a2d5ab
> color name p2_4 #E5EFC1
Color 'p2_4' is opaque: rgb(89.8%, 93.7%, 75.7%) hex: #e5efc1
> hide #!5 models
> select #6.13
909 atoms, 900 bonds, 133 residues, 1 model selected
> transparency surface 40 sel
Missing or invalid "percent" argument: Expected a number
> transparency sel 40 surfaces
> select clear
> undo
> ~ribbon sel
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!5 models
> cartoon style modeHelix tube
> hide #!5 models
> lighting soft
> lighting simple
> ribbon sel
> ~surface sel
> surface sel
> ~ribbon sel
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> view name side
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/uS13m.cxs
> select clear
> view side
> show #!1 models
> hide #!1 models
> lighting soft
> view side
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/uS13m.cxs
> lighting flat
> show #!1 models
> view name side
> lighting soft
> lighting flat
> view side
> lighting soft
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_Hs_soft.png
> width 3000 height 2182 supersample 3 transparentBackground true
> lighting flat
> view side
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_Hs_flat.png
> width 3000 height 2182 supersample 3 transparentBackground true
> hide #!1 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_flat.png
> width 3000 height 2182 supersample 3 transparentBackground true
> lighting soft
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_soft.png
> width 3000 height 2182 supersample 3 transparentBackground true
> show #!1 models
> view side
> turn y 180
> turn y 90
> lighting simple
> view name v1
> lighting flat
> lighting soft
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/detail_Ec_Hs_soft.png
> width 3000 height 2182 supersample 3 transparentBackground true
> lighting flat
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/detail_Ec_Hs_flat.png
> width 3000 height 2182 supersample 3 transparentBackground true
> select #6.13
909 atoms, 900 bonds, 133 residues, 2 models selected
> cofr sel
> turn y 180
> select clear
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/detail_180_Ec_Hs_flat.png
> width 3000 height 2182 supersample 3 transparentBackground true
> lighting full
> lighting soft
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/detail_180_Ec_Hs_soft.png
> width 3000 height 2182 supersample 3 transparentBackground true
> hide #!1 models
> lighting simple
> show #!5 models
> select #6.13
909 atoms, 900 bonds, 133 residues, 2 models selected
> ribbon sel
> ~surface sel
> select clear
> show #!1 models
> cartoon style modeHelix default
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/uS13m.cxs
> hide #!1 models
> ui mousemode right "translate selected models"
> select add #5
177122 atoms, 182802 bonds, 293 pseudobonds, 20809 residues, 91 models
selected
> view matrix models #5,1,0,0,6.2984,0,1,0,-2.2598,0,0,1,8.7731
> view matrix models #5,1,0,0,9.7859,0,1,0,-4.6402,0,0,1,12.578
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.9988,0.043722,0.022017,-6.2406,-0.044176,0.99881,0.020583,0.81371,-0.021091,-0.02153,0.99955,22.942
> select #5.54/DX:62
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
291 atoms, 298 bonds, 34 residues, 1 model selected
> select up
1196 atoms, 1231 bonds, 141 residues, 1 model selected
> cofr sel
> select clear
> select add #5
177122 atoms, 182802 bonds, 293 pseudobonds, 20809 residues, 91 models
selected
> view matrix models
> #5,0.99794,0.061826,0.017323,-9.811,-0.062556,0.99701,0.045329,-0.1011,-0.014468,-0.046319,0.99882,28.197
> view matrix models
> #5,0.99602,0.04647,0.076047,-18.054,-0.055751,0.99061,0.12486,-17.14,-0.06953,-0.1286,0.98926,64.156
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99602,0.04647,0.076047,-15.098,-0.055751,0.99061,0.12486,-12.648,-0.06953,-0.1286,0.98926,60.795
> view matrix models
> #5,0.99602,0.04647,0.076047,-13.368,-0.055751,0.99061,0.12486,-9.9377,-0.06953,-0.1286,0.98926,58.347
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99602,0.046484,0.076057,-13.371,-0.055765,0.99061,0.12485,-9.9321,-0.069539,-0.12859,0.98926,58.348
> view matrix models
> #5,0.99109,8.5388e-06,0.13322,-12.203,-0.016383,0.99242,0.12181,-18.402,-0.13221,-0.12291,0.98357,71.807
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99109,8.5388e-06,0.13322,-11.851,-0.016383,0.99242,0.12181,-18.731,-0.13221,-0.12291,0.98357,73.319
> view matrix models
> #5,0.99109,8.5388e-06,0.13322,-12.636,-0.016383,0.99242,0.12181,-19.432,-0.13221,-0.12291,0.98357,73.029
> view matrix models
> #5,0.99109,8.5388e-06,0.13322,-11.673,-0.016383,0.99242,0.12181,-18.653,-0.13221,-0.12291,0.98357,72.01
> hide #!5 models
> show #!5 models
> select clear
> ui mousemode right select
Drag select of 1028 residues
Drag select of 80 residues
Drag select of 831 residues
Drag select of 205 residues
> select clear
> color #5.32 paleblue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #5.32 lightblue
> color list
8 custom colors: c1
, c2
, c3
, c4
, p2_1
, p2_2
, p2_3
, and p2_4
.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color #5.54 pink
> ui tool show "Build Structure"
> color #5.54 lemonchiffon
> lighting soft
> lighting simple
> select #5.32/DB:1163
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #5.32/DB:1130
20 atoms, 19 bonds, 2 residues, 1 model selected
Alignment identifier is 5.32/DB
> select #5.32/DB:1130
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5.32/DB:1130-1163
273 atoms, 279 bonds, 34 residues, 1 model selected
> color sel royalblue
> select #5.54/DX:74
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #5.54/DX:37
15 atoms, 13 bonds, 2 residues, 1 model selected
Alignment identifier is 5.54/DX
> select #5.54/DX:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5.54/DX:37-74
320 atoms, 327 bonds, 38 residues, 1 model selected
> color sel tan
> color sel salmon
> color sel khaki
> color sel olive
> color sel gold
> color sel mediumvioletred
> color #5.54 lightpink
> color sel mediumvioletred
> view v1
> undo
Drag select of 207 residues
Drag select of 18 residues
> select #6
54421 atoms, 56148 bonds, 1975 pseudobonds, 6431 residues, 30 models selected
> select subtract #6.13
53512 atoms, 55248 bonds, 1975 pseudobonds, 6298 residues, 29 models selected
> hide sel & #6.2-12,14-21#!6.1 cartoons
> hide #!5 models
> show sel & #6.2-12,14-21#!6.1 atoms
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
Drag select of 14 residues
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> select #5
177122 atoms, 182802 bonds, 293 pseudobonds, 20809 residues, 91 models
selected
> select subtract #5.32,54
166778 atoms, 172202 bonds, 293 pseudobonds, 19557 residues, 89 models
selected
> hide sel cartoons
> show sel atoms
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!6 models
> transparency sel 100
> transparency sel 100 atoms
> transparency sel 50 atoms
> lighting soft
> lighting flat
> lighting soft
> lighting simple
> hide sel atoms
> surface sel
> transparency sel 80 surfaces
> transparency sel 50 surfaces
> lighting soft
> show #!6 models
> hide #!6 models
> lighting flat
> lighting soft
> select #5.7/CJ:614@CG
1 atom, 1 residue, 1 model selected
> select clear
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/Tb_S13.png
> width 3000 height 2182 supersample 3 transparentBackground true
> hide #!5 models
> show #!6 models
> select #6
54421 atoms, 56148 bonds, 1975 pseudobonds, 6431 residues, 29 models selected
> show #!5 models
> view name v2
> hide #!6 models
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/Tb_S13.png
> width 3000 height 2182 supersample 3 transparentBackground true
> show #!6 models
> hide #!5 models
> select subtract #6.13
53512 atoms, 55248 bonds, 1975 pseudobonds, 6298 residues, 29 models selected
> view v2
> hide sel & #6.2-12,14-21#!6.1 atoms
> show sel & #6.2-12,14-21#!6.1 surfaces
> transparency sel 50 surfaces
> select clear
> lighting soft
> transparency sel 90 surfaces
> select #6
54421 atoms, 56148 bonds, 1975 pseudobonds, 6431 residues, 29 models selected
> select subtract #6.13
53512 atoms, 55248 bonds, 1975 pseudobonds, 6298 residues, 49 models selected
> transparency sel 90 surfaces
> select clear
> undo
> color sel white surfaces
> transparency sel 50 surfaces
> select clear
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/Ec_S13.png
> width 3000 height 2182 supersample 3 transparentBackground true
> close sur
Expected a models specifier or a keyword
> hide #!6.1-21 surfaces
> show #!5 models
> hide #5.32,54#!5.1-31,33-53,55-63#!6.1-21 surfaces
> ui tool show "Side View"
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/Ec_Tb_S13.png
> width 3000 height 2182 supersample 3 transparentBackground true
> view list
Named views: side, v1, v2
> view side
> show #!1 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> ribbon #6
> view side
> cartoon style modeHelix tubes
Invalid "modeHelix" argument: Should be one of 'default', 'tube', or 'wrap'
> cartoon style modeHelix tube
> view side
Drag select of 127 residues
> cartoon style modeHelix default
> surface #1
> transparency #1 100 surfaces
> ~ribbon #1
Drag select of mS37_A2 SES surface, 8905 of 200914 triangles, RNA_AA SES
surface, 294190 of 3001286 triangles, bS6m_AE SES surface, 2561 of 190136
triangles, uS7m_AF SES surface, 16774 of 313164 triangles, uS11m_AI SES
surface, 42527 of 186812 triangles, 192 residues
> select clear
Drag select of mS38_A3 SES surface, 1747 of 136332 triangles, RNA_AA SES
surface, 98766 of 3001286 triangles, uS7m_AF SES surface, 265 of 313164
triangles, uS11m_AI SES surface, 794 of 186812 triangles, uS14m_AK SES
surface, 11253 of 170088 triangles, mS31_AY SES surface, 3998 of 190180
triangles, 79 residues
Drag select of RNA_AA SES surface, 3542 of 3001286 triangles, uS15m_AL SES
surface, 1097 of 266718 triangles, 10 residues
> select clear
> ui mousemode right translate
> transparency #1 80 surfaces
> color #1 grey surfaces
> color #1 grey white
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1 white surfaces
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting soft
> transparency #1 50 surfaces
> view side
> transparency #1 80 surfaces
> transparency #1 75 surfaces
> transparency #1 60 surfaces
> transparency #1 30 surfaces
> transparency #1 20 surfaces
> lighting flat
> lighting full
> lighting soft
> view side
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_Hs_surface_soft.png
> width 3000 height 2182 supersample 3 transparentBackground true
> lighting flat
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_Hs_surface_flat.png
> width 3000 height 2182 supersample 3 transparentBackground true
> lighting soft
> view v1
> save
> /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/detail_Ec_Hs_soft_v2.png
> width 3000 height 2182 supersample 3 transparentBackground true
> hide #!1 models
> show #!5 models
> close session
> open
> /Users/ondrejgahura/Work/Publications/Bnonstop_editing/ChimeraX/RESC-A.cxs
> format session
opened ChimeraX session
> view list
Named views: default
> view default
> lighting soft
> show #17 models
> hide #17 models
> open
> /Users/ondrejgahura/Work/Publications/Bnonstop_editing/AF_metacentrum/download-Q04cDMVwqsg9pVGIzGKsxeVT8gKHGfwwpZcswgutER6GCodjdRTDCLknw2MRlboU.zip
Unrecognized file suffix '.zip'
> open
> /Users/ondrejgahura/Work/Publications/Bnonstop_editing/AF_metacentrum/bnresc3corrected/relaxed_model_1_pred_0.pdb
Chain information for relaxed_model_1_pred_0.pdb #18
---
Chain | Description
A | No description available
> hide #18 models
> show #18 models
> matchmaker #18 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RESC3_corrected_meta_Colab, chain A (#16) with
relaxed_model_1_pred_0.pdb, chain A (#18), sequence alignment score = 3455.9
RMSD between 419 pruned atom pairs is 0.761 angstroms; (across all 688 pairs:
9.150)
> hide #16 models
> show #16 models
> select add #18
11132 atoms, 11223 bonds, 688 residues, 1 model selected
> color bfactor sel
11132 atoms, 688 residues, atom bfactor range 27.9 to 94.3
> hide #16 models
> show #16 models
> undo
> color sel yellow
> rename #18 RESC3_Bn_corrected_AF_meta
> hide #18 models
> view default
> save
> /Users/ondrejgahura/Work/Publications/Bnonstop_editing/ChimeraX/RESC-A.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.7.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,3
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: 16 GB
System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
OS Loader Version: 540.120.3~6
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 6 days 6:45
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 Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
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: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (3)
comment:1 by , 22 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection saving session |
comment:2 by , 22 months ago
| Status: | accepted → feedback |
|---|
Hi Ondrej,
Thanks for reporting this problem. It is typically difficult for us to debug garbage-collection problems, because garbage collection isn't something that ChimeraX calls directly but instead Python calls it whenever it feels it's appropriate. Nonetheless, if you were willing to supply your RESC-A.cxs session file and relaxed_model_1_pred_0.pdb PDB file there is some chance we might be able to reproduce the crash. But it's perfectly understandable that you might not want to.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
comment:3 by , 17 months ago
| Resolution: | → fixed |
|---|---|
| Status: | feedback → closed |
Fixed in 1.8 release candidate
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Reported by Ondrej Gahura