Opened 4 years ago

Last modified 3 years ago

#6063 assigned defect

ISOLDE: various errors

Reported by: jean-marc.jeckelmann@… 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

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  

> open
> /Users/jmjb/Documents/001_IBMM/12_Phenix/LAT2_4F2hc_D11vs_EMBL_2021/RealSpaceRefine_15/J476_LAT2__real_space_refined_015-coot-16.pdb

Chain information for J476_LAT2__real_space_refined_015-coot-16.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open
> /Users/jmjb/Documents/001_IBMM/12_Phenix/LAT2_4F2hc_D11vs_EMBL_2021/Volumes/cSPA_476/cryosparc_P3_J476_006_volume_map_sharp.mrc

Opened cryosparc_P3_J476_006_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 0.822, shown at level 0.107, step 1, values float32  

> clipper associate #2 toModel #1

Opened cryosparc_P3_J476_006_volume_map_sharp.mrc as #1.1.1.1, grid size
256,256,256, pixel 0.822, shown at level 0.315, step 1, values float32  
Chain information for J476_LAT2__real_space_refined_015-coot-16.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
  

> hide cartoons

> show cartoons

> hide atoms

> show atoms

[Repeated 1 time(s)]

> undo

> volume #1.1.1.1 level 0.2079

> volume #1.1.1.1 style image

> volume #1.1.1.1 style surface

> volume #1.1.1.1 color #00ffff5e

> volume #1.1.1.1 level 0.1899

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 46 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> hide HC

Loading residue template for GDS from internal database  
Traceback (most recent call last):  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 50, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 99, in
_update_unparameterised_residues_list  
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3143, in
find_residue_templates  
forcefield.loadFile(xf)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/forcefield.py", line 331, in loadFile  
self.registerResidueTemplate(template)  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 256, in
registerResidueTemplate  
template.graph = self.template_graph(template)  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 280, in template_graph  
labels = [a.element.atomic_number for a in atoms]  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 280, in <listcomp>  
labels = [a.element.atomic_number for a in atoms]  
AttributeError: 'NoneType' object has no attribute 'atomic_number'  
  
AttributeError: 'NoneType' object has no attribute 'atomic_number'  
  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 280, in  
labels = [a.element.atomic_number for a in atoms]  
  
See log for complete Python traceback.  
  

> select #1

16832 atoms, 17058 bonds, 1084 residues, 13 models selected  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2784, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 619, in __init__  
raise e  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 597, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc,  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1350, in __init__  
system = self._system = self._create_openmm_system(ff, top,  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1433, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2798, in start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 228, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 50, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 107, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 353, in
find_possible_templates  
tgraph = template.graph  
AttributeError: '_TemplateData' object has no attribute 'graph'  
  
AttributeError: '_TemplateData' object has no attribute 'graph'  
  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 353, in
find_possible_templates  
tgraph = template.graph  
  
See log for complete Python traceback.  
  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2784, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 619, in __init__  
raise e  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 597, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc,  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1350, in __init__  
system = self._system = self._create_openmm_system(ff, top,  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1433, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2798, in start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 228, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 50, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 107, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 353, in
find_possible_templates  
tgraph = template.graph  
AttributeError: '_TemplateData' object has no attribute 'graph'  
  
AttributeError: '_TemplateData' object has no attribute 'graph'  
  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 353, in
find_possible_templates  
tgraph = template.graph  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 4 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 11.6.3 (20G415)
      Kernel Version: Darwin 20.6.0
      Time since boot: 14:30

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        U3277WB:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
        Color LCD:
          Resolution: 2880 x 1800
          UI Looks like: 1440 x 900 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

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
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    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: various errors

comment:2 by Tristan Croll, 3 years ago

Sorry... seems this one fell off my radar. I realise it's a year old now, but is it still an issue?

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