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Opened 9 months ago
Closed 9 months ago
#16929 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.7.4-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202308300120 (2023-08-30 01:20:01 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 0x00007ff849a169c0 (most recent call first):
Garbage-collecting
File "", line 1219 in _handle_fromlist
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/place.py", line 68 in __init__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/place.py", line 680 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/place.py", line 680 in place_list
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/place.py", line 753 in __getitem__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1097 in _first_intercept_excluding_children
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1053 in first_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1075 in first_intercept_children
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1058 in first_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 674 in first_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 725 in _position_intercepts
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 692 in first_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1075 in first_intercept_children
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1058 in first_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 131 in first_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 852 in picked_object_on_segment
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 820 in picked_object
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/std_modes.py", line 781 in pause
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 630 in _mouse_pause
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 493 in mouse_pause_tracking
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 140 in _redraw_timer_callback
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 893 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 1044 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, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, 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, numpy.linalg.lapack_lite, 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 (total: 114)
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{
"uptime" : 180000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
"coalitionID" : 1769,
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"captureTime" : "2025-02-21 15:54:35.9591 +0530",
"incident" : "FA08E7F0-FD45-4B20-9E1A-73830AD7E7A8",
"pid" : 17568,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-19 19:33:06.6355 +0530",
"procStartAbsTime" : 158908190469653,
"procExitAbsTime" : 184042375970455,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8CF03F97-226A-53CF-8598-44E306385C29","thirdParty":true},
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"parentPid" : 1,
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"crashReporterKey" : "15D25DF0-7659-D181-E945-A179084794A0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 772,
"sleepWakeUUID" : "29C05638-5653-4087-A492-9B8EC402EE8A",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487187799\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffee3000-7fffffee4000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":17568},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487187799\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffee3000-7fffffee4000 [ 4K] r-x\/r-x SM=SHM ",
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"faultingThread" : 0,
"threads" : 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"name" : "HIToolbox"
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"threadTriggered" : {
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"logWritingSignature" : "db8e56799d06db74fcf7a56a7de50a5402d1f194",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
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{
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.dev202308300120 (2023-08-30)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/jbaral/Downloads/fold_mku_ligased_nhej_synapsis_2024_06_25_13_26-2/fold_mku_ligased_nhej_synapsis_2024_06_25_13_26_model_0.cif
Chain information for
fold_mku_ligased_nhej_synapsis_2024_06_25_13_26_model_0.cif #1
---
Chain | Description
A B C D | .
E | .
F G | .
H I | .
> show sidechain target ab
> style stick
Changed 16393 atom styles
> set bgColor white
> set bgColor black
> select /F:1-22
439 atoms, 488 bonds, 22 residues, 1 model selected
> select /E:1-759
5901 atoms, 6045 bonds, 759 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
fold_mku_ligased_nhej_synapsis_2024_06_25_13_26_model_0.cif_E SES surface
#1.1: minimum, -17.45, mean -1.13, maximum 15.33
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> select #1/a-d
8684 atoms, 8852 bonds, 1092 residues, 1 model selected
> hide sel atoms
> select /E:1-759
5901 atoms, 6045 bonds, 759 residues, 1 model selected
> rainbow sel
> select clear
> open "/Users/jbaral/Desktop/PDB/DNA synapse.pdb"
Chain information for DNA synapse.pdb #2
---
Chain | Description
A E | No description available
B F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
> select #2/G:1-19
588 atoms, 630 bonds, 19 residues, 1 model selected
> select #2/H:15-33
613 atoms, 664 bonds, 19 residues, 1 model selected
> select #2/I:1-22
684 atoms, 733 bonds, 22 residues, 1 model selected
> select #2/g-j
2593 atoms, 2794 bonds, 82 residues, 1 model selected
> select ~sel & ##selected
14482 atoms, 14626 bonds, 906 residues, 1 model selected
> hide sel atoms
> select #2/g-j
2593 atoms, 2794 bonds, 82 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!1 to #2 & sel
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 DNA synapse.pdb, chain I (#2) with
fold_mku_ligased_nhej_synapsis_2024_06_25_13_26_model_0.cif, chain F (#1),
sequence alignment score = 88
RMSD between 16 pruned atom pairs is 1.043 angstroms; (across all 22 pairs:
3.100)
> matchmaker #!1 to #2/G & sel pairing bs
Using Nucleic matrix instead of BLOSUM-62 to match to DNA synapse.pdb #2/G
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 DNA synapse.pdb, chain G (#2) with
fold_mku_ligased_nhej_synapsis_2024_06_25_13_26_model_0.cif, chain F (#1),
sequence alignment score = 84.4
RMSD between 16 pruned atom pairs is 1.047 angstroms; (across all 19 pairs:
2.809)
> hide sel atoms
> show sel cartoons
> show sel atoms
> style sel stick
Changed 2593 atom styles
> hide sel cartoons
> set bgColor white
> set bgColor black
> hide sel atoms
> show sel cartoons
> select add #2
17075 atoms, 17420 bonds, 988 residues, 1 model selected
> show sel cartoons
> set bgColor white
> select #1/a,b
4342 atoms, 4426 bonds, 546 residues, 1 model selected
> select #1/a,b,c,d
8684 atoms, 8852 bonds, 1092 residues, 1 model selected
> color sel gray
> select #2/a,b,c,d
7247 atoms, 7319 bonds, 453 residues, 1 model selected
> select #2/a,b,e,f
14482 atoms, 14626 bonds, 906 residues, 1 model selected
> color sel gray
> select nucleic-aciod
Expected an objects specifier or a keyword
> select nucleic-acid
4401 atoms, 4818 bonds, 170 residues, 2 models selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> hide sel cartoons
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show sel cartoons
> show sel atoms
> color sel bychain
> color sel byelement
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
fold_mku_ligased_nhej_synapsis_2024_06_25_13_26_model_0.cif_F SES surface
#1.2: minimum, -20.83, mean -10.82, maximum -1.22
Coulombic values for
fold_mku_ligased_nhej_synapsis_2024_06_25_13_26_model_0.cif_G SES surface
#1.3: minimum, -20.30, mean -10.81, maximum -1.32
Coulombic values for
fold_mku_ligased_nhej_synapsis_2024_06_25_13_26_model_0.cif_H SES surface
#1.4: minimum, -17.64, mean -10.44, maximum -0.59
Coulombic values for
fold_mku_ligased_nhej_synapsis_2024_06_25_13_26_model_0.cif_I SES surface
#1.5: minimum, -17.39, mean -10.43, maximum -0.58
Coulombic values for DNA synapse.pdb_G SES surface #2.1: minimum, -16.34, mean
-9.24, maximum -0.70
Coulombic values for DNA synapse.pdb_H SES surface #2.2: minimum, -16.40, mean
-8.64, maximum 2.56
Coulombic values for DNA synapse.pdb_I SES surface #2.3: minimum, -19.20, mean
-9.42, maximum 1.16
Coulombic values for DNA synapse.pdb_J SES surface #2.4: minimum, -18.05, mean
-9.06, maximum 2.95
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2 models
> select add #2
18883 atoms, 19444 bonds, 1076 residues, 10 models selected
> hide sel & #!1 surfaces
> molmap sel 2
Opened map 2 as #3, grid size 131,238,144, pixel 0.667, shown at level 0.187,
step 1, values float32
> close #3
> select add #2
18883 atoms, 19444 bonds, 1076 residues, 10 models selected
> select subtract #2
1808 atoms, 2024 bonds, 88 residues, 9 models selected
> select ~sel & ##selected
14585 atoms, 14897 bonds, 1851 residues, 1 model selected
> select #2/g-j
2593 atoms, 2794 bonds, 82 residues, 1 model selected
> show #!1 atoms
> undo
> select #2/g-j
2593 atoms, 2794 bonds, 82 residues, 1 model selected
> select #2/G:1-19
588 atoms, 630 bonds, 19 residues, 1 model selected
> select #2/g-j
2593 atoms, 2794 bonds, 82 residues, 1 model selected
> show #!1 cartoons
> undo
> select #2/g-j
2593 atoms, 2794 bonds, 82 residues, 1 model selected
> show #!2 models
> show sel cartoons
> hide #!1 models
> show #!1 models
> hide #!2 models
> select add #2
17075 atoms, 17420 bonds, 988 residues, 5 models selected
> show #!2 models
> hide #!1 models
> select subtract #2
4 models selected
> hide #!2 surfaces
> show #!1 models
> hide #!2 models
> select #1/e
5901 atoms, 6045 bonds, 759 residues, 1 model selected
> hide cartoons
> hide sel cartoons
> save /Users/jbaral/Desktop/image2.png supersample 3
> select #1/e-h
7244 atoms, 7545 bonds, 825 residues, 1 model selected
> color sel gray
> select add #1
16393 atoms, 16921 bonds, 1939 residues, 5 models selected
> show sel cartoons
> select #1/g,h,i,j
1369 atoms, 1536 bonds, 66 residues, 1 model selected
> color sel gray
> select ~sel
32099 atoms, 32805 bonds, 2861 residues, 2 models selected
> hide sel & #!1 cartoons
> select #1/f
439 atoms, 488 bonds, 22 residues, 1 model selected
> show sel cartoons
> select clear
> save /Users/jbaral/Desktop/image3.png supersample 3
> select #1/a,b
4342 atoms, 4426 bonds, 546 residues, 1 model selected
> color sel purple
> show sel cartoon'
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel cartoons
> save /Users/jbaral/Desktop/image4.png supersample 3
> select up
16393 atoms, 16921 bonds, 1939 residues, 1 model selected
> select down
4342 atoms, 4426 bonds, 546 residues, 6 models selected
> select #1/a,b
4342 atoms, 4426 bonds, 546 residues, 1 model selected
> show sel cartoons
> select #1/c,d
4342 atoms, 4426 bonds, 546 residues, 1 model selected
> color sel salmon
> show sel cartoons
> save /Users/jbaral/Desktop/image5.png supersample 3
> show sel cartoons
> select clear
> save /Users/jbaral/Desktop/image6.png supersample 3
> sel#1/a-d
Unknown command: sel#1/a-d
> select #1/a-d
8684 atoms, 8852 bonds, 1092 residues, 1 model selected
> hide sel cartoons
> select #1/a,b
4342 atoms, 4426 bonds, 546 residues, 1 model selected
> show sel surfaces
> select #1/c,d
4342 atoms, 4426 bonds, 546 residues, 1 model selected
> show sel surfaces
> lighting soft
> select clear
> lighting soft
> lighting shadows true intensity 0.5
> rotate 0 180
Unknown command: rotate 0 180
> rotate X 0 180
Unknown command: rotate X 0 180
> turn X 180
> turn y 180
> turn y 1 180
> select #1/E
5901 atoms, 6045 bonds, 759 residues, 1 model selected
> show sel cartoons
> cartoon style (#!1 & sel) modeHelix tube sides 20
> undo
> color sel gold
> color sel blue
> select #1/E 9-261
Expected a keyword
> select #1/E:9-261
1919 atoms, 1967 bonds, 253 residues, 1 model selected
> view sel
> color sel red
> select ~sel #1/E
Expected a keyword
> set bgColor black
> undo
> select #1/a-d
8684 atoms, 8852 bonds, 1092 residues, 1 model selected
> select #1/E:460:757
14 atoms, 13 bonds, 2 residues, 1 model selected
> view sel
> select #1/E:460-757
2317 atoms, 2371 bonds, 298 residues, 1 model selected
> view sel
> color sel red
> undo
> select #1/E:1-100
757 atoms, 776 bonds, 100 residues, 1 model selected
> view sel
> color sel red
> hide #!1 models
> show #!1 models
> select add #1
16393 atoms, 16921 bonds, 1939 residues, 7 models selected
> select subtract #1
9 models selected
> hide #!1 models
> show #!1 models
> view all
> select #1/E
5901 atoms, 6045 bonds, 759 residues, 1 model selected
> color sel green
> view sel surface
Expected an integer >= 1 or a keyword
> show sel surfaces
> select clear
> hide sel surfaces
> transparency sel 50
> transparency sel 0
> select clear
> transparency #1.1-9 50
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> transparency #1.1-9 0
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> select #1/E
5901 atoms, 6045 bonds, 759 residues, 1 model selected
> rainbow sel
> select clear
> hide #!1 surfaces
> hide #!1 cartoons
> select #1/f-i
1808 atoms, 2024 bonds, 88 residues, 1 model selected
> show sel cartoons
> color sel gray
> select clear
> set bgColor white
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> save /Users/jbaral/Desktop/image4.png supersample 3
> select #1/a,b
4342 atoms, 4426 bonds, 546 residues, 1 model selected
> show sel surfaces
> select #1/a,b
4342 atoms, 4426 bonds, 546 residues, 1 model selected
> hide sel surfaces
> save /Users/jbaral/Desktop/image5.png supersample 3
> select #1/a,b
4342 atoms, 4426 bonds, 546 residues, 1 model selected
> show sel surfaces
> save /Users/jbaral/Desktop/image6.png supersample 3
> select #1/c,d
4342 atoms, 4426 bonds, 546 residues, 1 model selected
> show sel surfaces
> save /Users/jbaral/Desktop/image7.png supersample 3
> select #1/a-d
8684 atoms, 8852 bonds, 1092 residues, 1 model selected
> transparency sel 50
> transparency sel 0
> select #1/E
5901 atoms, 6045 bonds, 759 residues, 1 model selected
> show sel cartoons
> save /Users/jbaral/Desktop/image8.png supersample 3
> open "/Users/jbaral/Library/CloudStorage/OneDrive-
> TheUniversityofMelbourne/Enigma/MD DNA synapse/2-Ala mutations/Alamut-
> mKu-21bpDNA-complexes/mKu-DNA-alamut-full length.pdb"
Summary of feedback from opening /Users/jbaral/Library/CloudStorage/OneDrive-
TheUniversityofMelbourne/Enigma/MD DNA synapse/2-Ala mutations/Alamut-
mKu-21bpDNA-complexes/mKu-DNA-alamut-full length.pdb
---
warning | CONECT record for nonexistent atom: 4225
Chain information for mKu-DNA-alamut-full length.pdb #3
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> ui tool show "Show Sequence Viewer"
> close #3
> open "/Users/jbaral/Library/CloudStorage/OneDrive-
> TheUniversityofMelbourne/Enigma/MD DNA synapse/2-Ala mutations/Alamut-
> mKu-21bpDNA-complexes/mKu-DNA-alamut-full length.pdb"
Summary of feedback from opening /Users/jbaral/Library/CloudStorage/OneDrive-
TheUniversityofMelbourne/Enigma/MD DNA synapse/2-Ala mutations/Alamut-
mKu-21bpDNA-complexes/mKu-DNA-alamut-full length.pdb
---
warning | CONECT record for nonexistent atom: 4225
Chain information for mKu-DNA-alamut-full length.pdb #3
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #1/F #1/G #2/I #3/C
Alignment identifier is 1
> select #3/C:1-21
419 atoms, 466 bonds, 21 residues, 1 model selected
> select #1/F-G:1 #2/I:1 #3/C:1
89 atoms, 93 bonds, 4 residues, 3 models selected
> select #1/F-G #2/I #3/C
1981 atoms, 2175 bonds, 87 residues, 3 models selected
> select add #1
17496 atoms, 18120 bonds, 1982 residues, 11 models selected
> select subtract #1
1103 atoms, 1199 bonds, 43 residues, 12 models selected
> select add #2
17494 atoms, 17886 bonds, 1009 residues, 3 models selected
> select subtract #2
419 atoms, 466 bonds, 21 residues, 5 models selected
> select add #3
5083 atoms, 5266 bonds, 588 residues, 1 model selected
> select subtract #3
Nothing selected
> select #1/F-G:1 #2/I:1 #3/C:1
89 atoms, 93 bonds, 4 residues, 3 models selected
> select #1/F-G #2/I #3/C
1981 atoms, 2175 bonds, 87 residues, 3 models selected
> select clear
> select add #3
5083 atoms, 5266 bonds, 588 residues, 1 model selected
> view sel
> select #3/A,B:21
10 atoms, 8 bonds, 2 residues, 1 model selected
> close #3
> open "/Users/jbaral/Library/CloudStorage/OneDrive-
> TheUniversityofMelbourne/Enigma/MD DNA synapse/2-Ala mutations/WT-
> mKu-21bpDNA-complexes/mKu-DNA-Wild.pdb"
Summary of feedback from opening /Users/jbaral/Library/CloudStorage/OneDrive-
TheUniversityofMelbourne/Enigma/MD DNA synapse/2-Ala mutations/WT-mKu-21bpDNA-
complexes/mKu-DNA-Wild.pdb
---
warning | CONECT record for nonexistent atom: 4345
Chain information for mKu-DNA-Wild.pdb #3
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> select #3/A,B:21
24 atoms, 24 bonds, 2 residues, 1 model selected
> view sel
> select add #3
5203 atoms, 5390 bonds, 588 residues, 1 model selected
> view sel
> hide #!1 models
> close #3
> show #!2 models
> view #2
> show #!1 models
> undo
> show #!1 models
> view all
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.dev202308300120 (2023-08-30)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
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: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.7.4 (22H420)
Kernel Version: Darwin 22.6.0
Time since boot: 8 days, 6 hours, 54 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
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: 2.2.1
Babel: 2.12.1
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: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.47.1
ChimeraX-AtomicLibrary: 10.0.8
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: 2.10.4
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202308300120
ChimeraX-CoreFormats: 1.1
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: 1.1.2
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
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9
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: 1.5.12
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: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.2
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: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
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-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: 1.31.4
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7.post1
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.42.1
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.0
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
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: 1.5.7
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.5
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
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
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
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: 2.4.1
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: 0.6.2
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: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.4
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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