Opened 4 years ago

Closed 3 years ago

#5900 closed defect (fixed)

ISOLDE: add real-space map: structure is None

Reported by: leonardotrosa@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Trying to associate real-space map with current model in isolde cause this error

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> open "/Users/leonardo/OneDrive/Work/IECB/ComM/Cryo/iNEXT
> 06-2021/Processing_ComM_iNEXT/ComM_DNA/maps/CS244/cryosparc_P1_J244_004_volume_map.mrc"
> format mrc

Opened cryosparc_P1_J244_004_volume_map.mrc as #1, grid size 500,500,500,
pixel 0.645, shown at level 0.0292, step 2, values float32  

> open "/Users/leonardo/OneDrive/Work/IECB/ComM/Cryo/iNEXT
> 06-2021/Processing_ComM_iNEXT/ComM_DNA/Phenix_ComM_DNA/new_phenix_ComM_DNA/PDBTools_14/ComM_real_space_refined_009.deposit_000_modified.cif"

Summary of feedback from opening
/Users/leonardo/OneDrive/Work/IECB/ComM/Cryo/iNEXT
06-2021/Processing_ComM_iNEXT/ComM_DNA/Phenix_ComM_DNA/new_phenix_ComM_DNA/PDBTools_14/ComM_real_space_refined_009.deposit_000_modified.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 323  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "17" near line 74  
Bad residue range for struct_conf "33" near line 90  
Bad residue range for struct_conf "53" near line 110  
Bad residue range for struct_conf "69" near line 126  
Bad residue range for struct_conf "70" near line 127  
38 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "K 3" near line 264  
Invalid sheet range for struct_sheet_range "L 1" near line 266  
Invalid sheet range for struct_sheet_range "L 2" near line 267  
Invalid sheet range for struct_sheet_range "L 3" near line 268  
Invalid sheet range for struct_sheet_range "M 1" near line 269  
6 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 46993  
  
Chain information for ComM_real_space_refined_009.deposit_000_modified.cif #2  
---  
Chain | Description  
A B D E F | No description available  
C | No description available  
Y | No description available  
Z | No description available  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1050, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2525, in _change_selected_model  
correct_pseudosymmetric_sidechain_atoms(session, m.residues)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 28, in
correct_pseudosymmetric_sidechain_atoms  
if flip_if_necessary(r, ('CD','NE','CZ',('NH2','NH1'))):  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 66, in flip_if_necessary  
if swap_equivalent_atoms(residue):  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 118, in swap_equivalent_atoms  
pair[0].coords, pair[1].coords = pair[1].coords, pair[0].coords  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 3 does not match objects array length 2  
  
Error processing trigger "add models":  
ValueError: Values array length 3 does not match objects array length 2  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  

> hide #!1 models

> close

> open "/Users/leonardo/OneDrive/Work/IECB/ComM/Cryo/iNEXT
> 06-2021/Processing_ComM_iNEXT/ComM_DNA/maps/CS244/cryosparc_P1_J244_004_volume_map.mrc"
> format mrc

Opened cryosparc_P1_J244_004_volume_map.mrc as #1, grid size 500,500,500,
pixel 0.645, shown at level 0.0292, step 2, values float32  

> open "/Users/leonardo/OneDrive/Work/IECB/ComM/Cryo/iNEXT
> 06-2021/Processing_ComM_iNEXT/ComM_DNA/Phenix_ComM_DNA/new_phenix_ComM_DNA/RealSpaceRefine_9/ComM_real_space_refined_009.pdb"

Chain information for ComM_real_space_refined_009.pdb #2  
---  
Chain | Description  
A B D E F | No description available  
C | No description available  
Y | No description available  
Z | No description available  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1050, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2525, in _change_selected_model  
correct_pseudosymmetric_sidechain_atoms(session, m.residues)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 28, in
correct_pseudosymmetric_sidechain_atoms  
if flip_if_necessary(r, ('CD','NE','CZ',('NH2','NH1'))):  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 66, in flip_if_necessary  
if swap_equivalent_atoms(residue):  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 118, in swap_equivalent_atoms  
pair[0].coords, pair[1].coords = pair[1].coords, pair[0].coords  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 3 does not match objects array length 2  
  
Error processing trigger "add models":  
ValueError: Values array length 3 does not match objects array length 2  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1496, in
_add_real_space_map_from_gui  
self.add_real_space_map(existing_volume=v, to_model=self.selected_model)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1386, in add_real_space_map  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 183, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1496, in
_add_real_space_map_from_gui  
self.add_real_space_map(existing_volume=v, to_model=self.selected_model)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1386, in add_real_space_map  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 183, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
File "/Users/leonardo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.31
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G9323)
      Kernel Version: Darwin 18.7.0
      Time since boot: 7:13

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        LG UltraFine:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 806NTKF1F589
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
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    snowballstemmer: 2.2.0
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    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: add real-space map: structure is None

Reported by Leonardo Talachia Rosa

comment:2 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

Very sorry about the super-slow response, but this is now fixed.

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