Crash when coordinate values in PDB file are not numbers

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.1-x86_64-i386-64bit
ChimeraX Version: 1.7rc202311210052 (2023-11-21 00:52:06 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 0x0000000110eb0600 (most recent call first):
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1345 in apply_auto_styling
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 192 in added_to_session
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1263 in added_to_session
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 756 in add
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 294 in provider_open
  File "/Applications/ChimeraX-1.7-rc2023.11.21.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-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/Applications/ChimeraX-1.7-rc2023.11.21.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-rc2023.11.21.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-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 464 in cxcmd
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 446 in defer
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 375 in thread_safe
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 455 in chimerax_intercept
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 353 in intercept
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 93 in _intercept
  File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 320 in interceptRequest
  File "/Applications/ChimeraX-1.7-rc2023.11.21.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-rc2023.11.21.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-rc2023.11.21.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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 52)


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{
  "uptime" : 13000,
  "procLaunch" : "2023-11-22 11:04:31.6190 +0900",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
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  "captureTime" : "2023-11-22 11:04:40.3196 +0900",
  "incident" : "F6587C37-B646-4F08-92BC-A5AF7A99B21D",
  "bug_type" : "309",
  "pid" : 20745,
  "procExitAbsTime" : 13533819316100,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7-rc2023.11.21.app\/Contents\/MacOS\/ChimeraX",
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  "storeInfo" : {"deviceIdentifierForVendor":"439D2673-AF12-5C08-B6BE-84082EF41D1B","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "C5083AD2-D586-23F5-635B-E196DC85081F",
  "sip" : "enabled",
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  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000002, 0x00007ff7b48ceff8","rawCodes":[2,140701862785016],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_PROTECTION_FAILURE at 0x00007ff7b48ceff8"},
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  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.7rc202311210052 (2023-11-21)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/home/dock/vina64/complex_u.pdb

Summary of feedback from opening /Users/home/dock/vina64/complex_u.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2023-11-04T13:10:36Z  
  
Ignored bad PDB record found on line 3  
  
  
Ignored bad PDB record found on line 1665  
REMARK 7 active torsions:  
  
Ignored bad PDB record found on line 1666  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
258 messages similar to the above omitted  
note |
/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py:414: RuntimeWarning: overflow
encountered in cast  
xyzr[:, :3] = atoms.coords  
  

Failed opening file /Users/home/dock/vina64/complex_u.pdb:  
Some X/Y/Z coordinate values in the 'complex_u.pdb' PDB file are not numbers  

> open /Users/home/dock/vina64/complex_u1.pdb format pdb

Summary of feedback from opening /Users/home/dock/vina64/complex_u1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2023-11-04T13:10:36Z  
  
Ignored bad PDB record found on line 1665  
REMARK 7 active torsions:  
  
Ignored bad PDB record found on line 1666  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 1667  
REMARK 1 A between atoms: C_13 and C_14  
  
257 messages similar to the above omitted  
notes | Combining 2 symmetry atoms into SER /A:410 H  
Combining 2 symmetry atoms into LEU /A:458 3HD1  
Combining 392 symmetry atoms into MET /A:379 H  
Combining 207 symmetry atoms into MET /A:379 CA  
Combining 53 symmetry atoms into LYS /A:380 N  
Combining 67 symmetry atoms into MET /A:379 O  
Combining 3 symmetry atoms into MET /A:379 SD  
Combining 2 symmetry atoms into GLY /A:411 HA3  
Combining 2 symmetry atoms into VAL /A:448 2HG2  
Combining 2 symmetry atoms into PRO /A:419 HD2  
Combining 2 symmetry atoms into VAL /A:417 1HG1  
  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.7rc202311210052 (2023-11-21)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/home/dock/vina64/complex_u.pdb

Summary of feedback from opening /Users/home/dock/vina64/complex_u.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2023-11-04T13:10:36Z  
  
Ignored bad PDB record found on line 3  
  
  
Ignored bad PDB record found on line 1665  
REMARK 7 active torsions:  
  
Ignored bad PDB record found on line 1666  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
258 messages similar to the above omitted  
note |
/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py:414: RuntimeWarning: overflow
encountered in cast  
xyzr[:, :3] = atoms.coords  
  

Failed opening file /Users/home/dock/vina64/complex_u.pdb:  
Some X/Y/Z coordinate values in the 'complex_u.pdb' PDB file are not numbers  




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OpenGL vendor: Intel Inc.

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Qt runtime version: 6.3.2
Qt platform: cocoa
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      Number of Processors: 1
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      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 447.60.3.0.0
      OS Loader Version: 540.60.2~89
      SMC Version (system): 2.43f11

Software:

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      Kernel Version: Darwin 21.2.0
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      Vendor: Intel
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      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
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          Framebuffer Depth: 24-Bit Color (ARGB8888)
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    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: 1.2.1
    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
    ChimeraX-PDB: 2.7.2
    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: 4.45.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.3
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.4
    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: 5.5.0
    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: 2.8.7
    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: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.0.0
    prompt-toolkit: 3.0.41
    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: 25.1.1
    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
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    sphinxcontrib-blockdiag: 3.0.0
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    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[pett]

User first opens a PDB file with NaNs in it, which ChimeraX rejects. Then opens a PDB file with hundreds of atoms with no bonds with various identical XYZ positions (hence the "Combining N symmetry atoms" messages. These are supposedly amino acid atoms! This structure eventually causes ChimeraX to crash in find_close_points during autostyling.

[Tom Goddard]

Wish I had a test case. find_close_points() should never crash even with lots of identical positions. Maybe I'll try to make a test case.

[Tom Goddard]

There is find_close_points() C++ code that explicitly looks for the points all being on top of each other to head off an infinite recursion. But I guess it is not handling every case. I'll see if I can break it. It is looking for a box containing a subset of points reaching size 0. The size 0 test is asymmetric looking at only one of the two boxes of points it is considering and that might be where the bug lies.

[pett]

The "combined" atoms will not be on top of each other -- they have been combined into a single atom. But since only atoms with no bonds get combined, there certainly are probably still many others on top of each other in this structure.

[Tom Goddard]

I see the problem that caused find_close_points() to crash. It was handed x,y,z coordinates containing the value IEEE Inf. The PDB code checks for NaN and refuses to load those files. The coordinates are handed to find_close_points() as float32 but the atomic coordinates are represented as float64. If a coordinate value exceeds the maximum float32 size 1e37 then numpy converts it to Inf and find_close_points() can't subdivide the boxes containing the points and crashes. I could put it checks for Inf values but I didn't want to slow down find_close_points() by checking all the input coordinates. Probably it could be checked more efficiently by just checking box bounds that are already computed to see if they are Inf. But I think this is sufficiently rare that I'm not going to put in those checks now. Maybe in the future I will add them so I don't have to debug this again.

[pett]

Perhaps I should change the test in pdb.py from "isnan(m.atoms.coords).any()" to "not isfinite(m.atoms.coords).all()"? What do you think?

[goddard@…]

I would leave the test as is.  I suspect the problem in this ticket was a number like 1e50 which is not going to be detected as Inf since float64 has a range of 1e300.  It is only when we cast it down to float32 that trouble ensues.  I'm not sure if the PDB reader would allow an "Inf" in an atom site line.  We know it reads NaN, but I'm not sure about Inf.  And I've never seen a PDB file contain Inf so don't know that is worth testing.  I guess molecular dynamics that explodes can produce these absurd coordinates.

[pett]

It seems unlikely that the coordinates are that large. There are only 7 columns available to represent each coordinate component. It seems more likely to me that those columns literally had "Inf" or "-Inf" in them. Unless you think my change would be actively harmful somehow, I'm inclined to make it...

[pett]

I guess the columns could have had "1e50" in them. I think the sprintf family reads the same values it writes, so I assume it can read infinity. Still, I see no reason not to screen out infinite coordinates...

[Tom Goddard]

I'm not against the change. But is isinfinite() true for NaN? I would guess no. Also I think "not isinfinite(coords).all()" as a test to reject a PDB would only let through ones with all infinite coordinates, probably not the best!

I was envisioning nasty MD PDB files with exponential notation, literally "1.23e50" in the coordinate columns. But who knows.

[pett]

infinite() is False for both infinite values and NaNs. The test is of which to _reject_, so therefore "not isfinite(...).all()"

[goddard@…]

I get isfinite, not isinfinite!  Got it.

[pett]

Made the change.