Illegal PDB file

[francisco.murphy@…]

The following bug report has been submitted:
Platform:        Linux-6.6.13-200.fc39.x86_64-x86_64-with-glibc2.38
ChimeraX Version: 1.8.dev202401281842 (2024-01-28 18:42:33 UTC)
Description
Trying to open a superposition from mustang

Log:
UCSF ChimeraX version: 1.8.dev202401281842 (2024-01-28)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open superposition.pdb

Summary of feedback from opening superposition.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Produced by MUSTANG v3.2.4  
  
Ignored bad PDB record found on line 2  
REMARK Authors: A S Konagurthu, J C Whisstock, P J Stuckey, and A M Lesk  
  
Ignored bad PDB record found on line 4  
REMARK Structures: 2VB1.pdb 7P6M.pdb 7YRK.pdb 3LZT.pdb  
  
Ignored bad PDB record found on line 39  
REMARK All structures were superposed on the coordinate frame of: 2VB1.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
267997 messages similar to the above omitted  
Ignored bad PDB record found on line 274039  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/core/__main__.py", line 885, in init  
commands.run(sess, 'open %s' % StringArg.unparse(arg))  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 294, in provider_open  
session.models.add(opened_models)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/core/models.py", line 761, in add  
m.added_to_session(session)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1280, in added_to_session  
self._report_chain_descriptions(session)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1546, in
_report_chain_descriptions  
self._report_chain_summary(session, descripts, chain_text, False)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1718, in _report_chain_summary  
cids = ' '.join([chain_text(chain) for chain in chains])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1718, in <listcomp>  
cids = ' '.join([chain_text(chain) for chain in chains])  
^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1545, in chain_text  
chain_res_range(chain), (chain.chain_id if not chain.chain_id.isspace() else
'?'))  
^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1793, in chain_res_range  
return range_string(first, last)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1789, in range_string  
return "%s-%s" % (first.string(residue_only=first_res_only, style="command"),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "atomic_cpp/cymol.pyx", line 1751, in
chimerax.atomic.cymol.CyResidue.string  
File "atomic_cpp/cymol.pyx", line 1064, in
chimerax.atomic.cymol.CyResidue.chain_id.__get__  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 0:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 0:
invalid start byte  
  
File "atomic_cpp/cymol.pyx", line 1064, in
chimerax.atomic.cymol.CyResidue.chain_id.__get__  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.3.3
OpenGL renderer: Mesa Intel(R) Xe Graphics (TGL GT2)
OpenGL vendor: Intel

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

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: LENOVO
Model: 82FE
OS: Fedora Linux 39 Workstation Edition
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.6Gi       2.9Gi       2.1Gi       559Mi       3.4Gi       4.6Gi
	Swap:          7.6Gi       731Mi       6.8Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation TigerLake-LP GT2 [Iris Xe Graphics] [8086:9a49] (rev 01)	
	Subsystem: Lenovo Device [17aa:3f18]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.5.1
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.15
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.52
    ChimeraX-AtomicLibrary: 12.1.10
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    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: 2.11
    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: 1.4
    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: 1.8.dev202401281842
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.1
    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: 1.1.9
    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
    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: 2.6.2
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.2
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    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-NMRSTAR: 1.0.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.2
    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: 1.2.1
    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: 2.11.1
    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: 1.15
    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: 1.33.5
    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
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.5
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    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: 3.1.3
    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: 4.3.3
    MarkupSafe: 2.1.4
    matplotlib: 3.8.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.7
    ndindex: 1.7
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.3
    openvr: 1.26.701
    packaging: 23.2
    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: 5.9.7
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynmrstar: 3.3.2
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3301
    pyparsing: 3.1.1
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.4
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.4
    setuptools: 67.4.0
    sfftk-rw: 0.8.1
    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: 3.9.2
    tcia-utils: 1.5.1
    tifffile: 2023.12.9
    tinyarray: 1.2.4
    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
File attachment: superposition.pdb

superposition.pdb​

[francisco.murphy@…]

Added by email2trac

[pett]

Hi Francisco,

As per the PDB standard, chain IDs have to be alphanumeric. Starting with line 61259 of the file, Mustang starts using non-alphanumeric chain IDs, and starting with line 113614 the chain IDs aren't even ASCII characters anymore! There is no way ChimeraX will be able to use this PDB file.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[francisco.murphy@…]

Thanks Eric.
Can chimerax align hundreds of PDBs? (I guess that will depend on the size
of the PDBs and the memory of the computer?)



El mié, 31 ene 2024 a la(s) 1:25 p.m., ChimeraX (
ChimeraX-bugs-admin@cgl.ucsf.edu) escribió:

>
>
>
>
>
>

[pett]

Assuming ChimeraX can open the hundreds of structures (which in not necessarily a given), aligning them should not be too much of a problem (though it could take a few minutes). Let's say you open 500 structures (in model numbers 1-500), then you could align them with "mm #2-500 to #1".

--Eric