Crash splitting molecule

[gabriel.alves2@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-27-generic-x86_64-with-glibc2.35
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

Current thread 0x00007f32a025fb80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 243 in set_c_pointer
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 108 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2403 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 279 in atom_bonds
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 233 in molecule_from_atoms
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 100 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 100 in split_molecule
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 63 in split
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/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.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mlp._mlp, chimerax.coulombic._esp (total: 56)
===== 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 /home/dynamics/Downloads/4kly.pdb format pdb

4kly.pdb title:  
Crystal structure of A blue-light absorbing proteorhodopsin mutant D97N from
HOT75 [more info...]  
  
Chain information for 4kly.pdb #1  
---  
Chain | Description | UniProt  
A B C D E | BPR | PRRB_PRB02 0-250  
  
Non-standard residues in 4kly.pdb #1  
---  
RET — retinal  
  

> set bgColor white

> show cartoons

> hide atoms

> slit

Unknown command: slit  

> split

Split 4kly.pdb (#1) into 5 models  
Chain information for 4kly.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 4kly.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 4kly.pdb C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 4kly.pdb D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 4kly.pdb E #1.5  
---  
Chain | Description  
E | No description available  
  

> hide #!1.5 models

> hide #!1.4 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.4 models

> hide #!1.4 models

> show #!1.5 models

> hide #!1.5 models

> lighting soft

> lighting full

> lighting simple

> lighting shadows true

> graphics silhouettes true

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting flat

> lighting soft

> save "/home/dynamics/Área de Trabalho/Crystal structure of a blue-light
> absorbing proteorhodopsin mutant D97N from HOT75 2monomeros.png" width 1291
> height 803 supersample 3

> show #!1.2 models

> hide #!1.1 models

> color #1.2 #813d9cff

> color #1.2 #613583ff

> color #1.2 #c061cbff

> color #1.2 #dc8addff

> color #1.2 #3584e4ff

> color #1.2 #1a5fb4ff

> color #1.2 mediumpurple

> color #1.2 #3d3846ff

> color #1.2 #9141acff

> color #1.2 #813d9cff

> color #1.2 #613583ff

> color #1.2 #c061cbff

> color #1.2 #dc8addff

> color #1.2 #99c1f1ff

> color #1.2 #62a0eaff

> color #1.2 #3584e4ff

> color #1.2 #1c71d8ff

> color #1.2 #1a5fb4ff

> color #1.2 #9141acff

> color #1.2 mediumpurple

> color #1.2 #c061cbff

> color #1.2 #9141acff

> color #1.2 #813d9cff

> color #1.2 #613583ff

> color #1.2 mediumpurple

> color #1.2 #613583ff

> color #1.2 mediumpurple

> ui tool show H-Bonds

> hbonds intraMol false intraRes false reveal true

34 hydrogen bonds found  

> hbonds saltOnly true intraMol false reveal true

0 hydrogen bonds found  

> hbonds sel saltOnly true intraMol false reveal true

Atom specifier selects no atoms  

> hbonds sel saltOnly true reveal true

Atom specifier selects no atoms  

> show #!1.1 models

> hide #!1.1 models

> show #!1.4 models

> hbonds intraMol false intraRes false reveal true

34 hydrogen bonds found  

> hbonds intraModel false intraMol false intraRes false reveal true

0 hydrogen bonds found  

> hbonds intraModel false intraMol false intraRes false reveal true

0 hydrogen bonds found  

> hbonds intraModel false intraMol false intraRes false reveal true

0 hydrogen bonds found  

> ui tool show Contacts

> contacts resSeparation 5 intraRes true intraModel false ignoreHiddenModels
> true color #ee1d00 radius 0.035

No contacts  

> contacts resSeparation 5 intraRes true intraModel false ignoreHiddenModels
> true color #ee1d00 radius 0.035

No contacts  

> contacts ignoreHiddenModels true

4150 contacts  

> contacts intraModel false ignoreHiddenModels true

No contacts  

> contacts intraRes true intraModel false ignoreHiddenModels true

No contacts  

> contacts intraModel false

No contacts  

> contacts

6864 contacts  

> contacts intraModel false intraMol false

No contacts  

> contacts sel intraModel false intraMol false

No atoms match given atom specifier  

> contacts sel restrict cross intraModel false intraMol false

No atoms match given atom specifier  

> contacts sel restrict both intraModel false intraMol false

No atoms match given atom specifier  
Restriction atom specifier must not be blank  

> contacts bondSeparation 5 intraModel false intraMol false

No contacts  

> contacts bondSeparation 3 intraModel false intraMol false

No contacts  

> contacts intraModel false intraMol false

No contacts  

> contacts distanceOnly 4.0 intraModel false intraMol false

No distances  

> contacts intraModel false intraMol false makePseudobonds false

No contacts  

> contacts intraModel false intraMol false continuous true

No contacts  

> contacts intraModel false intraMol false

No contacts  

> ~contacts

> contacts intraModel false intraMol false

No contacts  

> contacts intraModel false intraMol false

No contacts  

> hbonds #!1.2-4 reveal true

745 hydrogen bonds found  

> ~hbonds

> hide #!1.2-4 atoms

> hide #!1.4 models

> ui mousemode right select

Drag select of 230 residues  

> hbonds sel reveal true

298 hydrogen bonds found  

> mlp sel

Map values for surface "4kly.pdb C_C SES surface": minimum -25.94, mean
0.2008, maximum 42.62  
Map values for surface "4kly.pdb B_B SES surface": minimum -26.75, mean
0.4923, maximum 39.69  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 4kly.pdb B_B SES surface #1.2.3: minimum, -14.79, mean
-1.48, maximum 8.24  
Coulombic values for 4kly.pdb C_C SES surface #1.3.3: minimum, -15.53, mean
-1.53, maximum 10.13  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> hide sel atoms

> ~hbonds

Drag select of 100 atoms, 462 residues, 2 pseudobonds  

> hide sel atoms

> set bgColor black

> ui mousemode right select

> style sel ball

Changed 3544 atom styles  

> set bgColor white

> close session

> open /home/dynamics/Downloads/7bu7.pdb format pdb

7bu7.pdb title:  
Structure of human Β1 adrenergic receptor bound to Bi-167107 and nanobody 6B9
[more info...]  
  
Chain information for 7bu7.pdb #1  
---  
Chain | Description | UniProt  
A | endolysin,endolysin,β-1 adrenergic receptor chimera | D9IEF7_BPT4 892-1051  
B | camelid antibody fragment |  
  
Non-standard residues in 7bu7.pdb #1  
---  
1WV — (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate  
CLR — cholesterol  
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)  
GLC — α-D-glucopyranose (α-D-glucose; D-glucose; glucose)  
NA — sodium ion  
P0G —
8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one  
P6G — hexaethylene glycol (polyethylene glycol PEG400)  
SO4 — sulfate ion  
  

> close session

> open /home/dynamics/Downloads/7jjo.pdb format pdb

7jjo.pdb title:  
Structural basis of the activation of heterotrimeric GS-protein by
isoproterenol-bound Β1-adrenergic receptor [more info...]  
  
Chain information for 7jjo.pdb #1  
---  
Chain | Description | UniProt  
A | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-380  
B | transducin β chain 1 | GBB1_BOVIN 2-340  
G | G γ-I | GBG2_BOVIN 1-71  
N | nanobody 35 |  
R | Β1-adrenergic receptor |  
  
Non-standard residues in 7jjo.pdb #1  
---  
5FW — isoprenaline  
  

> hide atoms

> show cartoons

> select /N

1909 atoms, 1931 bonds, 128 residues, 1 model selected  

> hide sel cartoons

> split


===== 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  




OpenGL version: 3.3.0 NVIDIA 535.86.10
OpenGL renderer: NVIDIA GeForce RTX 3080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: pt_BR.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 13th Gen Intel(R) Core(TM) i5-13400F
Cache Size: 20480 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       5.0Gi        22Gi       175Mi       4.1Gi        25Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3080 Lite Hash Rate] [10de:2216] (rev a1)	
	Subsystem: PNY GA102 [GeForce RTX 3080 Lite Hash Rate] [196e:136d]	
	Kernel driver in use: nvidia

Installed Packages:
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    backcall: 0.2.0
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    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
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    ChimeraX-Contacts: 1.0.1
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    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
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    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-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
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    ChimeraX-MapFit: 2.0
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    ChimeraX-Mask: 1.0.2
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    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
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    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
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    ChimeraX-Positions: 1.0
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    ChimeraX-PubChem: 2.1
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    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
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    ChimeraX-RenumberResidues: 1.1
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    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
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    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
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    ChimeraX-STL: 1.0.1
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    ChimeraX-SwapAA: 2.0.1
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    ChimeraX-TapeMeasure: 1.0
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    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
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    ChimeraX-VIPERdb: 1.0
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    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
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    setuptools: 67.4.0
    sfftk-rw: 0.7.3
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    sphinxcontrib-devhelp: 1.0.6
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    sphinxcontrib-serializinghtml: 1.1.10
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    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
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    typing-extensions: 4.9.0
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File attachment: 7jjo.pdb

7jjo.pdb​

[gabriel.alves2@…]

Added by email2trac

[Tom Goddard]

It is not clear to me why ChimeraX crashed when you were trying to split a molecule into separate chains. My best guess is that it is a known bug in ChimeraX 1.7.1 where Python garbage collection (freeing memory for deleted objects) crashes. That bug often strikes after closing a session and then doing some more operations (probably because closing the session causes many objects to be garbage collected). This was fixed in the current ChimeraX daily build. So if you are seeing other crashes you might want to try the ChimeraX daily build.