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Opened 18 months ago
Closed 18 months ago
#15145 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-12.7.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000148f1000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000112a8e600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py", line 576 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1613 in remove_deleted_pointers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 134 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 807 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 171 in check_residues
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 41 in assign_charges
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 56)
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"procName" : "ChimeraX",
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"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
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"arch" : "x86_64",
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"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
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"arch" : "x86_64",
"base" : 4517556224,
"size" : 64094208,
"uuid" : "9d768904-ac4b-327d-8126-cec11a08b966",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 4256K 8 \nCG image 272K 21 \nColorSync 236K 28 \nCoreAnimation 160K 14 \nCoreGraphics 16K 3 \nCoreServices 932K 4 \nCoreUI image data 4276K 32 \nFoundation 68K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.5G 271 \nMALLOC guard page 48K 9 \nMALLOC_MEDIUM (reserved) 240.0M 4 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 104K 26 \nStack 171.7M 27 \nStack Guard 56.0M 1 \nVM_ALLOCATE 334.8M 283 \n__CTF 756 1 \n__DATA 59.0M 679 \n__DATA_CONST 31.1M 342 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 677.6M 155 \n__OBJC_RO 82.9M 1 \n__OBJC_RW 3200K 2 \n__TEXT 809.3M 681 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 191.0M 47 \nshared memory 3500K 26 \n=========== ======= ======= \nTOTAL 4.3G 2900 \nTOTAL, minus reserved VM space 3.9G 2900 \n",
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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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/pcarlton/Downloads/fold_2024_05_09_10_36phosdsb_1_wdna/fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif
Chain information for fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif #1
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
> hide atoms
> show cartoons
> lighting shadows false
> lighting simple
> set bgColor white
> set bgColor black
> select /F:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
455 atoms, 455 bonds, 55 residues, 1 model selected
> select add /E:111
464 atoms, 463 bonds, 56 residues, 1 model selected
> select up
910 atoms, 910 bonds, 110 residues, 1 model selected
Alignment identifier is 1
> select clear
> select /E:118
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /F:107
20 atoms, 18 bonds, 2 residues, 1 model selected
> select up
910 atoms, 910 bonds, 110 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #f500e7 radius 0.2 dashes 0 interModel false intraRes false
> select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif
137 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A TYR 307 OH /F GLU 93 OE1 no hydrogen 2.053 N/A
/B TYR 307 OH /E GLU 93 OE1 no hydrogen 2.028 N/A
/B ARG 311 NH2 /E GLU 93 OE1 no hydrogen 2.849 N/A
/E CYS 83 SG /F GLY 234 O no hydrogen 3.632 N/A
/E SER 84 OG /F ASP 9 OD1 no hydrogen 2.613 N/A
/E SER 84 OG /F ASP 9 OD2 no hydrogen 3.450 N/A
/E ARG 86 NE /B ASP 304 OD1 no hydrogen 3.226 N/A
/E ARG 86 NH2 /B SEP 199 O no hydrogen 2.486 N/A
/E LEU 87 N /E CYS 83 O no hydrogen 2.947 N/A
/E ALA 88 N /E SER 84 O no hydrogen 3.023 N/A
/E VAL 89 N /E MET 85 O no hydrogen 3.084 N/A
/E LEU 90 N /E ARG 86 O no hydrogen 3.039 N/A
/E GLU 91 N /E LEU 87 O no hydrogen 2.923 N/A
/E ILE 92 N /E ALA 88 O no hydrogen 3.051 N/A
/E GLU 93 N /E VAL 89 O no hydrogen 3.095 N/A
/E ARG 94 N /E LEU 90 O no hydrogen 2.920 N/A
/E ARG 94 NH1 /B SEP 204 O3P no hydrogen 3.097 N/A
/E ARG 94 NH2 /B SEP 204 O3P no hydrogen 2.521 N/A
/E ARG 94 NH2 /B SEP 209 O2P no hydrogen 3.374 N/A
/E GLN 95 N /E GLU 91 O no hydrogen 2.887 N/A
/E GLU 96 N /E ILE 92 O no hydrogen 2.920 N/A
/E THR 97 N /E GLU 93 O no hydrogen 2.907 N/A
/E THR 97 OG1 /E GLU 93 O no hydrogen 2.672 N/A
/E ALA 98 N /E ARG 94 O no hydrogen 2.825 N/A
/E MET 99 N /E GLN 95 O no hydrogen 2.809 N/A
/E LYS 100 N /E GLU 96 O no hydrogen 2.968 N/A
/E LYS 101 N /E THR 97 O no hydrogen 3.008 N/A
/E LYS 102 N /E ALA 98 O no hydrogen 2.788 N/A
/E GLU 103 N /E MET 99 O no hydrogen 2.958 N/A
/E GLU 104 N /E LYS 100 O no hydrogen 2.989 N/A
/E SER 105 N /E LYS 101 O no hydrogen 2.814 N/A
/E LYS 106 N /E LYS 102 O no hydrogen 2.751 N/A
/E ARG 107 N /E GLU 103 O no hydrogen 2.934 N/A
/E GLN 108 N /E GLU 104 O no hydrogen 2.779 N/A
/E LYS 109 N /E SER 105 O no hydrogen 2.646 N/A
/E ILE 110 N /E LYS 106 O no hydrogen 3.171 N/A
/E LYS 111 N /E ARG 107 O no hydrogen 3.385 N/A
/E LYS 112 N /E GLN 108 O no hydrogen 2.721 N/A
/E LYS 112 NZ /E GLN 108 OE1 no hydrogen 2.774 N/A
/E THR 113 N /E LYS 109 O no hydrogen 2.763 N/A
/E THR 113 N /E ILE 110 O no hydrogen 3.292 N/A
/E THR 113 OG1 /E LYS 109 O no hydrogen 2.528 N/A
/E GLU 115 N /E LYS 111 O no hydrogen 3.151 N/A
/E ARG 116 N /E LYS 112 O no hydrogen 2.711 N/A
/E LYS 117 N /E THR 113 O no hydrogen 3.112 N/A
/E LYS 118 N /E LYS 114 O no hydrogen 3.262 N/A
/E HIS 119 N /E GLU 115 O no hydrogen 2.812 N/A
/E ALA 120 N /E ARG 116 O no hydrogen 2.701 N/A
/E ILE 121 N /E LYS 117 O no hydrogen 3.050 N/A
/E GLN 122 N /E LYS 118 O no hydrogen 3.036 N/A
/E ALA 123 N /E HIS 119 O no hydrogen 2.752 N/A
/E ALA 124 N /E ALA 120 O no hydrogen 2.859 N/A
/E LYS 125 N /E ILE 121 O no hydrogen 3.058 N/A
/E THR 126 N /E GLN 122 O no hydrogen 2.888 N/A
/E THR 126 OG1 /E GLN 122 O no hydrogen 2.973 N/A
/E ARG 127 N /E ALA 123 O no hydrogen 2.813 N/A
/E LYS 128 N /E ALA 124 O no hydrogen 2.890 N/A
/E GLN 129 N /E LYS 125 O no hydrogen 2.916 N/A
/E ARG 130 N /E THR 126 O no hydrogen 2.823 N/A
/E ASN 131 N /E ARG 127 O no hydrogen 2.905 N/A
/E ASN 131 ND2 /H DC 10 OP2 no hydrogen 2.719 N/A
/E GLU 132 N /E LYS 128 O no hydrogen 2.908 N/A
/E ILE 133 N /E GLN 129 O no hydrogen 2.853 N/A
/E GLU 134 N /E ARG 130 O no hydrogen 2.786 N/A
/E GLU 135 N /E ASN 131 O no hydrogen 2.782 N/A
/E ALA 136 N /E GLU 132 O no hydrogen 2.933 N/A
/E SER 137 N /E ILE 133 O no hydrogen 2.757 N/A
/E SER 137 OG /E ILE 133 O no hydrogen 2.576 N/A
/E GLN 138 N /E GLU 134 O no hydrogen 3.023 N/A
/E ARG 142 NH1 /E GLU 135 OE1 no hydrogen 3.551 N/A
/E ARG 145 NH2 /E GLU 134 OE1 no hydrogen 2.611 N/A
/F CYS 83 SG /E GLY 234 O no hydrogen 3.414 N/A
/F SER 84 OG /E ASP 9 OD1 no hydrogen 2.290 N/A
/F SER 84 OG /E ASP 9 OD2 no hydrogen 3.183 N/A
/F ARG 86 NE /A ASP 304 OD1 no hydrogen 2.876 N/A
/F ARG 86 NH2 /A VAL 203 O no hydrogen 2.419 N/A
/F LEU 87 N /F CYS 83 O no hydrogen 2.943 N/A
/F ALA 88 N /F SER 84 O no hydrogen 3.021 N/A
/F VAL 89 N /F MET 85 O no hydrogen 3.103 N/A
/F LEU 90 N /F ARG 86 O no hydrogen 3.025 N/A
/F GLU 91 N /F LEU 87 O no hydrogen 2.924 N/A
/F ILE 92 N /F ALA 88 O no hydrogen 3.059 N/A
/F GLU 93 N /F VAL 89 O no hydrogen 3.126 N/A
/F ARG 94 N /F LEU 90 O no hydrogen 2.937 N/A
/F ARG 94 NH1 /A SEP 204 O3P no hydrogen 3.195 N/A
/F ARG 94 NH2 /A SEP 204 O3P no hydrogen 2.483 N/A
/F GLN 95 N /F GLU 91 O no hydrogen 2.889 N/A
/F GLU 96 N /F ILE 92 O no hydrogen 2.939 N/A
/F THR 97 N /F GLU 93 O no hydrogen 2.936 N/A
/F THR 97 OG1 /F GLU 93 O no hydrogen 2.687 N/A
/F ALA 98 N /F ARG 94 O no hydrogen 2.816 N/A
/F MET 99 N /F GLN 95 O no hydrogen 2.801 N/A
/F LYS 100 N /F GLU 96 O no hydrogen 2.991 N/A
/F LYS 101 N /F THR 97 O no hydrogen 3.040 N/A
/F LYS 102 N /F ALA 98 O no hydrogen 2.794 N/A
/F GLU 103 N /F MET 99 O no hydrogen 2.974 N/A
/F GLU 104 N /F LYS 100 O no hydrogen 3.007 N/A
/F SER 105 N /F LYS 101 O no hydrogen 2.826 N/A
/F LYS 106 N /F LYS 102 O no hydrogen 2.789 N/A
/F ARG 107 N /F GLU 103 O no hydrogen 2.981 N/A
/F GLN 108 N /F GLU 104 O no hydrogen 2.803 N/A
/F LYS 109 N /F SER 105 O no hydrogen 2.664 N/A
/F ILE 110 N /F LYS 106 O no hydrogen 3.237 N/A
/F LYS 111 N /F ARG 107 O no hydrogen 3.425 N/A
/F LYS 112 N /F GLN 108 O no hydrogen 2.747 N/A
/F LYS 112 NZ /F GLN 108 OE1 no hydrogen 2.801 N/A
/F THR 113 N /F LYS 109 O no hydrogen 2.807 N/A
/F THR 113 N /F ILE 110 O no hydrogen 3.293 N/A
/F THR 113 OG1 /F LYS 109 O no hydrogen 2.572 N/A
/F GLU 115 N /F LYS 111 O no hydrogen 3.171 N/A
/F ARG 116 N /F LYS 112 O no hydrogen 2.732 N/A
/F LYS 117 N /F THR 113 O no hydrogen 3.163 N/A
/F LYS 118 N /F LYS 114 O no hydrogen 3.291 N/A
/F HIS 119 N /F GLU 115 O no hydrogen 2.829 N/A
/F ALA 120 N /F ARG 116 O no hydrogen 2.736 N/A
/F ILE 121 N /F LYS 117 O no hydrogen 3.078 N/A
/F GLN 122 N /F LYS 118 O no hydrogen 3.064 N/A
/F ALA 123 N /F HIS 119 O no hydrogen 2.770 N/A
/F ALA 124 N /F ALA 120 O no hydrogen 2.881 N/A
/F LYS 125 N /F ILE 121 O no hydrogen 3.083 N/A
/F THR 126 N /F GLN 122 O no hydrogen 2.918 N/A
/F THR 126 OG1 /F GLN 122 O no hydrogen 3.002 N/A
/F ARG 127 N /F ALA 123 O no hydrogen 2.832 N/A
/F LYS 128 N /F ALA 124 O no hydrogen 2.918 N/A
/F GLN 129 N /F LYS 125 O no hydrogen 2.956 N/A
/F ARG 130 N /F THR 126 O no hydrogen 2.852 N/A
/F ASN 131 N /F ARG 127 O no hydrogen 2.936 N/A
/F ASN 131 ND2 /G DC 10 OP2 no hydrogen 3.191 N/A
/F GLU 132 N /F LYS 128 O no hydrogen 2.950 N/A
/F ILE 133 N /F GLN 129 O no hydrogen 2.875 N/A
/F GLU 134 N /F ARG 130 O no hydrogen 2.813 N/A
/F GLU 135 N /F ASN 131 O no hydrogen 2.813 N/A
/F ALA 136 N /F GLU 132 O no hydrogen 2.970 N/A
/F SER 137 N /F ILE 133 O no hydrogen 2.807 N/A
/F SER 137 OG /F ILE 133 O no hydrogen 2.626 N/A
/F GLN 138 N /F GLU 134 O no hydrogen 3.062 N/A
/F ARG 145 NH2 /F GLU 134 OE1 no hydrogen 2.688 N/A
137 hydrogen bonds found
> style sel ball
Changed 258 atom styles
> select up
1121 atoms, 1109 bonds, 131 residues, 1 model selected
> style sel ball
Changed 1121 atom styles
> select clear
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
> select clear
> select /G-H:1-2
86 atoms, 94 bonds, 4 residues, 1 model selected
> select /G-H:1-43
1766 atoms, 1976 bonds, 86 residues, 1 model selected
> select clear
> select /A-B:186
20 atoms, 18 bonds, 2 residues, 1 model selected
> select /A-B:186
20 atoms, 18 bonds, 2 residues, 1 model selected
> close #1.1
> show sel atoms
> style sel sphere
Changed 20 atom styles
> color sel byhetero
> select clear
Drag select of 7 residues
Drag select of 15 residues
> select up
846 atoms, 851 bonds, 112 residues, 1 model selected
> select up
7523 atoms, 7683 bonds, 945 residues, 1 model selected
> hide sel cartoons
Drag select of 14 residues
> select up
482 atoms, 490 bonds, 64 residues, 1 model selected
> select up
3055 atoms, 3127 bonds, 385 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 2 residues
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select up
2817 atoms, 2865 bonds, 345 residues, 1 model selected
> rainbow sel
Drag select of 4 residues
> select up
216 atoms, 220 bonds, 26 residues, 1 model selected
> select up
2817 atoms, 2865 bonds, 345 residues, 1 model selected
> rainbow sel
> select clear
Drag select of 21 residues
> select up
380 atoms, 382 bonds, 45 residues, 1 model selected
> select up
5634 atoms, 5730 bonds, 690 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif_E SES
surface #1.1: minimum, -19.54, mean -0.18, maximum 15.79
Coulombic values for fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif_F SES
surface #1.2: minimum, -18.71, mean -0.20, maximum 15.51
To also show corresponding color key, enter the above coulombic command and
add key true
> show sel cartoons
> select clear
> select /A-B:285-286
30 atoms, 30 bonds, 4 residues, 1 model selected
> select /A-B:285-385
1632 atoms, 1662 bonds, 202 residues, 1 model selected
> show sel cartoons
> select /C-D:201
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /C-D:201-280
1298 atoms, 1324 bonds, 160 residues, 1 model selected
> show sel cartoons
> select clear
> show cartoons
> select clear
Drag select of fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif_F SES surface,
35405 of 414852 triangles, 16 atoms, 43 residues, 13 bonds
> select clear
> select /E-F:100
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E-F:100-119
358 atoms, 358 bonds, 40 residues, 1 model selected
> set bgColor white
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/pcarlton/Desktop/movie3.mp4
Movie saved to /Users/pcarlton/Desktop/movie3.mp4
> close
> open
> /Users/pcarlton/Downloads/fold_2024_05_09_10_36phosdsb_1_wdna/fold_2024_05_09_10_36phosdsb_1_wdna_model_1.cif
Chain information for fold_2024_05_09_10_36phosdsb_1_wdna_model_1.cif #1
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
> hide atoms
> show cartoons
Drag select of 3 residues
> select up
438 atoms, 438 bonds, 52 residues, 1 model selected
> select up
2817 atoms, 2865 bonds, 345 residues, 1 model selected
> select up
18062 atoms, 18610 bonds, 2110 residues, 1 model selected
> select down
2817 atoms, 2865 bonds, 345 residues, 1 model selected
> select add /F:110
2825 atoms, 2872 bonds, 346 residues, 1 model selected
> select up
3249 atoms, 3297 bonds, 396 residues, 1 model selected
> select up
5634 atoms, 5730 bonds, 690 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2024_05_09_10_36phosdsb_1_wdna_model_1.cif_E SES
surface #1.1: minimum, -17.65, mean -0.16, maximum 19.29
Coulombic values for fold_2024_05_09_10_36phosdsb_1_wdna_model_1.cif_F SES
surface #1.2: minimum, -17.58, mean -0.16, maximum 18.76
To also show corresponding color key, enter the above coulombic command and
add key true
> open
> /Users/pcarlton/Downloads/fold_2024_05_09_10_36dsb_123_wdna/fold_2024_05_09_10_36dsb_123_wdna_model_0.cif
Chain information for fold_2024_05_09_10_36dsb_123_wdna_model_0.cif #2
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
> hide #!1 models
> close #1
> hide atoms
> show cartoons
> select /F:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /E:135
14 atoms, 12 bonds, 2 residues, 1 model selected
> select up
874 atoms, 874 bonds, 104 residues, 1 model selected
> select up
5634 atoms, 5730 bonds, 690 residues, 1 model selected
> coulombic sel
===== 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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/pcarlton/Downloads/fold_2024_05_09_11_32_scerec114x4_mei4x2_dna/fold_2024_05_09_11_32_scerec114x4_mei4x2_dna_model_0.cif
Chain information for fold_2024_05_09_11_32_scerec114x4_mei4x2_dna_model_0.cif
#1
---
Chain | Description
A B C D | .
E F | .
G H | .
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon R9 M380 OpenGL Engine
OpenGL vendor: ATI Technologies 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: iMac
Model Identifier: iMac17,1
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 32 GB
System Firmware Version: 522.0.0.0.0
OS Loader Version: 540.120.3~37
SMC Version (system): 2.33f12
Software:
System Software Overview:
System Version: macOS 12.7.1 (21G920)
Kernel Version: Darwin 21.6.0
Time since boot: 8 days 21:10
Graphics/Displays:
AMD Radeon R9 M380:
Chipset Model: AMD Radeon R9 M380
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x6640
Revision ID: 0x0080
ROM Revision: 113-C6005R-800
VBIOS Version: 113-C6005T-009
EFI Driver Version: 01.00.800
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
EV2336W:
Resolution: 1080 x 1920
UI Looks like: 1080 x 1920
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 80101073
Mirror: Off
Online: Yes
Rotation: 90
Installed Packages:
alabaster: 0.7.16
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: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 1.7.1
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: 2.6.1
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: 1.5.14
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: 1.0.4
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: 1.12.4
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: 1.33.3
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: 0.2.1
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: 4.47.2
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: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
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: 10.2.0
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: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
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: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 18 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 , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Peter,
--Eric