Error fetching CCD

[lee.yang@…]

The following bug report has been submitted:
Platform:        macOS-14.3.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Scenario: Using ISOLDE and attempting to rebuild residues to a CCD template. The fetching of most (but not all) templates generates an error (screenshot example).

Troubleshooting: Network config? Error occurs when connected either through my residential internet connection, or routed through my work VPN. Fetching of molecules from the CCD using "open <ccd_id> from ccd" works.

I contacted Tristan, who pointed out the relevant ChimeraX mmcif.find_template_residue() code.

If not a network issue, is it perhaps due to any recent changes to the CCD template nomenclature? 

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> functionkey F1 'ui tool show "Models"'

> functionkey F2 'ui tool show "Volume Viewer"'

> functionkey F3 'ui tool show "Log"'

> functionkey F4 'ui tool show "ISOLDE"'

> functionkey F5 'lighting soft; set bgColor white'

> functionkey F6 'lighting simple; set bgColor black'

> mousemode alt rightMode "center or translate"

> mousemode alt leftMode "translate selected models"

> mousemode alt wheelMode "play map series"

> alias clear log clear

> alias ca close all

> alias ta tile all

> alias ~ta ~tile all

> alias show_1 show #1 models; alias t1 hide_1

> alias hide_1 hide #1 models; alias t1 show_1

> alias show_2 show #2 models; alias t2 hide_2

> alias hide_2 hide #2 models; alias t2 show_2

> alias show_3 show #3 models; alias t3 hide_3

> alias hide_3 hide #3 models; alias t3 show_3

> alias show_4 show #4 models; alias t4 hide_4

> alias hide_4 hide #4 models; alias t4 show_4

> alias show_5 show #5 models; alias t5 hide_5

> alias hide_5 hide #5 models; alias t5 show_5

> alias show_6 show #6 models; alias t6 hide_6

> alias hide_6 hide #6 models; alias t6 show_6

> alias show_7 show #7 models; alias t7 hide_7

> alias hide_7 hide #7 models; alias t7 show_7

> alias show_8 show #8 models; alias t8 hide_8

> alias hide_8 hide #8 models; alias t8 show_8

> show_1

> show_2

> show_3

> show_4

> show_5

> show_6

> show_7

> show_8

> alias hide_h select #$1; select intersect H; hide sel atoms

> alias show_h select #$1; select intersect H; show sel atoms

> alias sp cofr centerofview showpivot true

> alias ~sp cofr centerofview showpivot false

> alias add_pivot sp; buttonpanel Shortcuts add Pivot[-] command
> "remove_pivot" row 1 column 3

> alias remove_pivot ~sp; buttonpanel Shortcuts add Pivot[+] command
> "add_pivot" row 1 column 3

> alias mark marker #20000 position cofr

> alias helix setattr $1 res is_helix true

> alias strand setattr $1 res is_strand true

> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias clipexpand clip near -2 far 2

> alias clipreduce clip near 2 far -2

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.12; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue; rbc #*

> alias cootmode_mesh set bgColor black; surface cap false; surface style
> mesh; lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball;
> style ions ball; size ballscale 0.2; size stickradius 0.12; cofr
> centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> #3d60ffff; transparency 50; rbc #*

> alias default_map set bgColor black; surface cap true; surface style solid;
> lighting simple; graphics silhouettes false; ~clip; size stickradius 0.2;
> size ballscale 0.3; color ##~num_residues #b2b2b2ff; transparency 0; preset
> "initial styles" "original look"

> alias rbc rainbow $1; color $1 byhetero

> alias trigger_cootm cootmode_mesh; buttonpanel Shortcuts add Coot[-] command
> "trigger_cootn" row 1 column 1

> alias trigger_cootn default_map; buttonpanel Shortcuts add Coot[m] command
> "trigger_cootm" row 1 column 1

> alias vstart vseries play #$1 startTime 0 direction oscillate loop true
> normalize true pauseFrames 1

> alias vstop vseries stop #$1

> alias start_play vstart *; buttonpanel Shortcuts add V[stop] command
> "stop_play" row 2 column 5

> alias stop_play vstop *; buttonpanel Shortcuts add V[start] command
> "start_play" row 2 column 5

> alias smooth vol #* surfacesmoothing 1 subdividesurface 1 subdivisionLevels
> 1

> alias nosmooth vol #* surfacesmooth 0 subdividesurface 0

> alias trigger_smooth smooth; buttonpanel Shortcuts add Sm[-] command
> "trigger_nosmooth" row 2 column 2

> alias trigger_nosmooth nosmooth; buttonpanel Shortcuts add Sm[+] command
> "trigger_smooth" row 2 column 2

> alias reset trigger_cootn; trigger_nosmooth

> buttonpanel Shortcuts rows 2 columns 5

> buttonpanel Shortcuts add Vseries command "open browse vseries true" row 1
> column 5

> buttonpanel Shortcuts add V[start] command start_play row 2 column 5

> buttonpanel Shortcuts add Coot[m] command trigger_cootm row 1 column 1

> buttonpanel Shortcuts add RBC command "rbc #*" row 2 column 1

> buttonpanel Shortcuts add Step1 command "vol #* step 1" row 1 column 2

> buttonpanel Shortcuts add Sm[+] command trigger_smooth row 2 column 2

> buttonpanel Shortcuts add Pivot[+] command add_pivot row 1 column 3

> buttonpanel Shortcuts add MatchM command "ui tool show Matchmaker" row 2
> column 3

> buttonpanel Shortcuts add Clip[+] command clipreduce row 1 column 4

> buttonpanel Shortcuts add Clip[-] command clipexpand row 2 column 4

> cd /Users/ylee/Documents/chimerax

Current working directory is: /Users/ylee/Documents/chimerax  

> tools show "Models"

Error running startup command 'ui tools show "Models"': Unknown command: ui
tools show "Models"  
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/ylee/Documents/chimerax/temp.pdb

Chain information for temp.pdb #1  
---  
Chain | Description  
E | No description available  
P | No description available  
R | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for temp.pdb  
---  
Chain | Description  
1.2/E | No description available  
1.2/P | No description available  
1.2/R | No description available  
  
Fetching CCD PCA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/PCA/PCA.cif  
Fetching CCD HY3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/HY3/HY3.cif  
Fetching CCD AYA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/AYA/AYA.cif  
Fetching CCD CSO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CSO/CSO.cif  
Fetching CCD ORN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ORN/ORN.cif  
Fetching CCD CSS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/CSS/CSS.cif  

> open Y01 fromDatabase ccd

Summary of feedback from opening Y01 fetched from ccd  
---  
note | Fetching CCD Y01 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/Y01/Y01.cif  
  
Y01 title:  
cholesterol hemisuccinate  
  
Opened CCD Y01  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

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: MacBook Pro
      Model Identifier: MacBookPro18,4
      Model Number: G15KLZP/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.81.1
      OS Loader Version: 10151.81.1

Software:

    System Software Overview:

      System Version: macOS 14.3.1 (23D60)
      Kernel Version: Darwin 23.3.0
      Time since boot: 29 days, 15 hours, 43 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U2722DE:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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-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-ISOLDE: 1.7.1
    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
File attachment: SCR-20240331-kxzi.png

SCR-20240331-kxzi.png​

[lee.yang@…]

Added by email2trac

[Eric Pettersen]

Probably related to #14853