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Opened 17 months ago
Closed 17 months ago
#15286 closed defect (duplicate)
Crash in garbage collection
| 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-14.3.1-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
Thread 0x00000003123de000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000201018240 (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/addh/cmd.py", line 1014 in to_h36
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 1084 in _h_name
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 949 in new_hydrogen
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 910 in add_altloc_hyds
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 909 in _attach_hydrogens
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 764 in add_hydrogens
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 184 in hbond_add_hydrogens
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 77 in cmd_addh
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 95 in assign_charges
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
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/shortcuts/shortcuts.py", line 525 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
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, lxml._elementpath, lxml.etree, chimerax.map._map, openmm._openmm, openmm.app.internal.compiled, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 62)
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{
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"codeSigningMonitor" : 1,
"incident" : "473186FF-AB06-4FBA-A810-66D8019F2301",
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"procLaunch" : "2024-05-23 21:42:09.1204 +0100",
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"procExitAbsTime" : 4743767330994,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
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"wakeTime" : 5885,
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"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140723170197335\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffcaa924000-7ffcd36d4000 [653.7M] r-x\/r-x SM=COW ...t_id=489a6acf",
"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":80221},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140723170197335\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffcaa924000-7ffcd36d4000 [653.7M] r-x\/r-x SM=COW ...t_id=489a6acf",
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"faultingThread" : 0,
"threads" : 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"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=3.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 68K 17 \nColorSync 240K 30 \nCoreAnimation 340K 82 \nCoreGraphics 32K 5 \nCoreGraphics (reserved) 8K 1 reserved VM address space (unallocated)\nCoreUI image data 1552K 22 \nFoundation 40K 2 \nKernel Alloc Once 8K 1 \nMALLOC 2.5G 126 \nMALLOC guard page 384K 24 \nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1572K 390 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 860K 86 \nRosetta Thread Context 860K 86 \nSTACK GUARD 40K 10 \nStack 179.1M 42 \nStack Guard 56.1M 32 \nVM_ALLOCATE 293.2M 417 \nVM_ALLOCATE (reserved) 256.1M 17 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 57.4M 861 \n__DATA_CONST 48.6M 455 \n__DATA_DIRTY 1866K 236 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 177.4M 184 \n__OBJC_RO 71.1M 1 \n__OBJC_RW 2170K 2 \n__TEXT 1.1G 864 \ndyld private memory 516K 4 \nmapped file 7.4G 1609 \nshared memory 3520K 25 \nunshared pmap 15.7M 11 \n=========== ======= ======= \nTOTAL 12.2G 5661 \nTOTAL, minus reserved VM space 12.0G 5661 \n",
"legacyInfo" : {
"threadTriggered" : {
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"queue" : "com.apple.main-thread"
}
},
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"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
},
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},
{
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}
],
"experiments" : [
{
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}
]
},
"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x7FF8A5482A78)"
]
}
===== 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 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb"
Chain information for B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb
#1
---
Chain | Description
A | No description available
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb"
Chain information for B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb
#2
---
Chain | Description
A | No description available
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb"
Chain information for B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb
#3
---
Chain | Description
A | No description available
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb"
Chain information for B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb
#4
---
Chain | Description
A | No description available
> select clear
> mmaker #2,3,4 to #1
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 B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb, chain A
(#1) with B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb, chain A
(#2), sequence alignment score = 845.9
RMSD between 67 pruned atom pairs is 1.241 angstroms; (across all 216 pairs:
12.206)
Matchmaker B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb, chain A
(#1) with B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb, chain A
(#3), sequence alignment score = 409.1
RMSD between 60 pruned atom pairs is 0.983 angstroms; (across all 199 pairs:
24.402)
Matchmaker B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb, chain A
(#1) with B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb, chain A
(#4), sequence alignment score = 387.3
RMSD between 85 pruned atom pairs is 1.144 angstroms; (across all 195 pairs:
41.074)
> select clear
> preset custom pretty-chain
Using preset: Custom / Pretty-chain
Preset expands to these ChimeraX commands:
lighting soft
set bgColor white
cartoon style coil width 1.5 thickness 0.8
cartoon style helix xsection round width 3 thickness 0.8
cartoon style strand xsection round width 3 thickness 0.8
cartoon style strand arrowscale 1
cartoon style helix xsection oval sides 10
graphics silhouettes true
graphics silhouettes width 1.5
graphics silhouettes depthJump 0.003
lighting msDepthBias 0.004
lighting shadows true intensity 0.06
lighting depthCueColor #000000
color bychain
Drag select of 166 residues
> hide sel cartoons
Drag select of 44 residues
> hide sel cartoons
Drag select of 150 residues
> hide sel cartoons
Drag select of 19 residues
> hide sel cartoons
Drag select of 26 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 39 residues
> hide sel cartoons
> select clear
Drag select of 432 residues
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb_A
SES surface #1.1: minimum, -24.37, mean -3.30, maximum 13.45
Coulombic values for B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb_A
SES surface #2.1: minimum, -20.31, mean -1.50, maximum 16.74
Coulombic values for B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb_A
SES surface #3.1: minimum, -23.13, mean -2.88, maximum 14.21
Coulombic values for B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb_A
SES surface #4.1: minimum, -17.29, mean -1.27, maximum 16.16
To also show corresponding color key, enter the above coulombic command and
add key true
> tile
4 models tiled
> select clear
> preset custom pretty-chain
Using preset: Custom / Pretty-chain
Preset expands to these ChimeraX commands:
lighting soft
set bgColor white
cartoon style coil width 1.5 thickness 0.8
cartoon style helix xsection round width 3 thickness 0.8
cartoon style strand xsection round width 3 thickness 0.8
cartoon style strand arrowscale 1
cartoon style helix xsection oval sides 10
graphics silhouettes true
graphics silhouettes width 1.5
graphics silhouettes depthJump 0.003
lighting msDepthBias 0.004
lighting shadows true intensity 0.06
lighting depthCueColor #000000
color bychain
Drag select of B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb_A SES
surface, 129886 of 311652 triangles,
B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb_A SES surface, 128941
of 330650 triangles, B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb_A
SES surface, 141145 of 302144 triangles,
B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb_A SES surface, 141317
of 288802 triangles, 432 residues
> coulombic sel
Coulombic values for B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb_A
SES surface #1.1: minimum, -24.37, mean -3.30, maximum 13.45
Coulombic values for B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb_A
SES surface #2.1: minimum, -20.31, mean -1.50, maximum 16.74
Coulombic values for B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb_A
SES surface #3.1: minimum, -23.13, mean -2.88, maximum 14.21
Coulombic values for B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb_A
SES surface #4.1: minimum, -17.29, mean -1.27, maximum 16.16
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> hide #!2 models
> show #!2 models
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb"
Chain information for A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb
#5
---
Chain | Description
A | No description available
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb"
Chain information for A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb
#6
---
Chain | Description
A | No description available
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb"
Chain information for A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb
#7
---
Chain | Description
A | No description available
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb"
Chain information for A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb
#8
---
Chain | Description
A | No description available
> close session
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb"
Chain information for A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb
#1
---
Chain | Description
A | No description available
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb"
Chain information for A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb
#2
---
Chain | Description
A | No description available
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb"
Chain information for A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb
#3
---
Chain | Description
A | No description available
> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/ESCRT/Sequences/AF/A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb"
Chain information for A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb
#4
---
Chain | Description
A | No description available
> mmaker #2,3,4 to #1
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 A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A
(#1) with A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb, chain A
(#2), sequence alignment score = 441.1
RMSD between 80 pruned atom pairs is 0.949 angstroms; (across all 198 pairs:
20.445)
Matchmaker A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A
(#1) with A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb, chain A
(#3), sequence alignment score = 363.8
RMSD between 53 pruned atom pairs is 1.083 angstroms; (across all 192 pairs:
27.603)
Matchmaker A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A
(#1) with A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb, chain A
(#4), sequence alignment score = 305.6
RMSD between 73 pruned atom pairs is 1.008 angstroms; (across all 197 pairs:
25.672)
> select clear
Drag select of 241 residues
> hide sel cartoons
Drag select of 64 residues
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 41 residues
> hide sel cartoons
Drag select of 20 residues
> hide sel cartoons
Drag select of 26 residues
> hide sel cartoons
Drag select of 21 residues
Drag select of 11 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
> select #4/A:148-1000
574 atoms, 580 bonds, 75 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 426 residues
> mmaker sel
> matchmaker sel
Missing required "to" argument
> mmaker sel to #1
Must use different reference and match structures
> hide #1 models
Drag select of 319 residues
> mmaker sel to #1
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 A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A
(#1) with A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb, chain A
(#2), sequence alignment score = 273.4
RMSD between 81 pruned atom pairs is 0.950 angstroms; (across all 107 pairs:
2.419)
Matchmaker A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A
(#1) with A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb, chain A
(#3), sequence alignment score = 241
RMSD between 65 pruned atom pairs is 0.954 angstroms; (across all 107 pairs:
5.443)
Matchmaker A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A
(#1) with A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb, chain A
(#4), sequence alignment score = 188.5
RMSD between 72 pruned atom pairs is 1.018 angstroms; (across all 92 pairs:
3.105)
> select clear
> show #1 models
Drag select of 426 residues
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
===== 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 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
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: Mac
Model Identifier: Mac14,5
Model Number: Z17J0018AB/A
Chip: Unknown
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 64 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 3 days, 27 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL P2717H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
DELL P2722H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
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-Clipper: 0.22.3
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-ISOLDE: 1.7
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 (2)
comment:1 by , 17 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 |
comment:2 by , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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