Opened 20 months ago

Closed 18 months ago

Last modified 18 months ago

#14661 closed defect (fixed)

PDB-REDO: Unknown polymer entity

Reported by: r.xie@… Owned by: Greg Couch
Priority: normal Milestone: 1.8
Component: Input/Output Version:
Keywords: Cc: pett, Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.5.0-18-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Chimerax can't correctly display catoons from mmcif files from PDB-REDO. However, all other softwares can display it without problem, such as ccp4mg and pymol.  In attachment, I supply a example mmcif files from PDB-REDO data bank. 

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 /home/r.xie/1cbs_final.cif format mmcif

Summary of feedback from opening /home/r.xie/1cbs_final.cif  
---  
warnings | Unknown polymer entity '1 1' near line 1370  
Skipping atom "CD" near line 1382: missing coordinates  
Skipping atom "NE" near line 1383: missing coordinates  
Skipping atom "CZ" near line 1384: missing coordinates  
Skipping atom "NH1" near line 1385: missing coordinates  
Skipping atom "NH2" near line 1386: missing coordinates  
4 messages similar to the above omitted  
Unknown polymer entity '1 2' near line 1457  
Skipping atom "CG" near line 1460: missing coordinates  
Skipping atom "CD" near line 1461: missing coordinates  
Skipping atom "CE" near line 1462: missing coordinates  
Skipping atom "NZ" near line 1463: missing coordinates  
Skipping atom "O" near line 1484: missing coordinates  
30 messages similar to the above omitted  
Unknown polymer entity '1 3' near line 1534  
Skipping atom "CB" near line 1536: missing coordinates  
Skipping atom "CG" near line 1537: missing coordinates  
Skipping atom "CD" near line 1538: missing coordinates  
Skipping atom "CE" near line 1539: missing coordinates  
Skipping atom "NZ" near line 1540: missing coordinates  
Unknown polymer entity '1 4' near line 1600  
Skipping atom "CG" near line 1663: missing coordinates  
Skipping atom "OD2" near line 1665: missing coordinates  
Unknown polymer entity '1 5' near line 1675  
Unknown polymer entity '1 6' near line 1760  
Skipping atom "N" near line 1810: missing coordinates  
Skipping atom "CA" near line 1811: missing coordinates  
Skipping atom "CB" near line 1812: missing coordinates  
Skipping atom "CG" near line 1813: missing coordinates  
Skipping atom "CD" near line 1814: missing coordinates  
23 messages similar to the above omitted  
Unknown polymer entity '1 7' near line 1839  
Skipping atom "N" near line 1839: missing coordinates  
Skipping atom "CA" near line 1840: missing coordinates  
Skipping atom "CB" near line 1841: missing coordinates  
Skipping atom "CG" near line 1842: missing coordinates  
Skipping atom "CD" near line 1843: missing coordinates  
23 messages similar to the above omitted  
Unknown polymer entity '1 8' near line 1923  
Skipping atom "N" near line 1923: missing coordinates  
Skipping atom "CA" near line 1924: missing coordinates  
Skipping atom "CB" near line 1925: missing coordinates  
Skipping atom "CG" near line 1926: missing coordinates  
Skipping atom "CD" near line 1927: missing coordinates  
67 messages similar to the above omitted  
Unknown polymer entity '1 9' near line 2004  
Skipping atom "N" near line 2004: missing coordinates  
Skipping atom "CA" near line 2005: missing coordinates  
Skipping atom "CB" near line 2006: missing coordinates  
Skipping atom "CG" near line 2007: missing coordinates  
Skipping atom "CD" near line 2008: missing coordinates  
48 messages similar to the above omitted  
Unknown polymer entity '1 10' near line 2086  
Skipping atom "N" near line 2086: missing coordinates  
Skipping atom "CA" near line 2087: missing coordinates  
Skipping atom "CB" near line 2088: missing coordinates  
Skipping atom "CG" near line 2089: missing coordinates  
Skipping atom "CD1" near line 2090: missing coordinates  
50 messages similar to the above omitted  
Unknown polymer entity '1 11' near line 2163  
Skipping atom "CD" near line 2185: missing coordinates  
Skipping atom "OE1" near line 2186: missing coordinates  
Skipping atom "OE2" near line 2187: missing coordinates  
Skipping atom "C" near line 2196: missing coordinates  
Skipping atom "O" near line 2197: missing coordinates  
27 messages similar to the above omitted  
Unknown polymer entity '1 12' near line 2242  
Skipping atom "CD1" near line 2247: missing coordinates  
Skipping atom "N" near line 2285: missing coordinates  
Skipping atom "CA" near line 2286: missing coordinates  
Skipping atom "CB" near line 2287: missing coordinates  
Skipping atom "CG" near line 2288: missing coordinates  
7 messages similar to the above omitted  
Unknown polymer entity '1 13' near line 2315  
Skipping atom "O" near line 2409: missing coordinates  
Skipping atom "O" near line 2420: missing coordinates  
Skipping atom "O" near line 2421: missing coordinates  
Skipping atom "O" near line 2424: missing coordinates  
Skipping atom "O" near line 2426: missing coordinates  
25 messages similar to the above omitted  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /A:48  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /A:85  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /A:85  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /A:91  
Atom CE has no neighbors to form bonds with according to residue template for
LYS /A:92  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /A:94  
Unable to fetch template for 'REA': will connect using distance criteria  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 1cbs_final.cif #1  
---  
Chain | Description  
A | No description available  
  

> show cartoons

> close #1




OpenGL version: 3.3.0 NVIDIA 525.147.05
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: bluechip Computer AG
Model: bluechip BUSINESSline individu
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen 9 5950X 16-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        11Gi        35Gi       463Mi        15Gi        49Gi
	Swap:             0B          0B          0B

Graphics:
	08:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3090] [10de:2204] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. GA102 [GeForce RTX 3090] [1043:87b3]	
	Kernel driver in use: nvidia

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: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    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-Clipper: 0.22.4
    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-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: 2.6.1
    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
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    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: 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: 23.3.2
    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
    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
File attachment: 1cbs_final.cif

1cbs_final.cif​

Attachments (1)

1cbs_final.cif​ (253.0 KB ) - added by r.xie@… 20 months ago.
Added by email2trac

Download all attachments as: .zip

Change History (5)

by r.xie@…, 20 months ago

Attachment: 1cbs_final.cif​ added

Added by email2trac

comment:1 by pett, 20 months ago

Cc: pett Tom Goddard added
Component: Unassigned → Input/Output
Milestone: → 1.8
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → PDB-REDO: Unknown polymer entity

comment:2 by pett, 20 months ago

Reported by Ren Xie

comment:3 by Greg Couch, 18 months ago

Resolution: → fixed
Status: assigned → closed

Fixed in daily release.

comment:4 by Greg Couch, 18 months ago

FYI, this is because 1cbs_final does not follow the PDBx/mmCIF styling rules and confuses ChimeraX by having an audit_conform table. Otherwise, only the files from the PDB have the audit_conform table, and that fact was used to turn on stylized parsing.

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