Opened 4 years ago

Closed 3 years ago

#6245 closed defect (fixed)

ISOLDE _show_selected_clash: 'residues' is empty

Reported by: chimerax-bug-report@… 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: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/mac/Documents/Projects/symetry/c7/c7_pl416_model/ApplyNCS_9/c7_pl416_apply_ncs_6_INPUT_C9_symm_0001_s.pdb

Summary of feedback from opening
/Users/mac/Documents/Projects/symetry/c7/c7_pl416_model/ApplyNCS_9/c7_pl416_apply_ncs_6_INPUT_C9_symm_0001_s.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 375
ASN A 402 1 28  
Start residue of secondary structure not found: HELIX 2 2 GLU A 406 ASN A 433
1 28  
Start residue of secondary structure not found: HELIX 3 3 GLU A 437 ASN A 464
1 28  
Start residue of secondary structure not found: HELIX 4 4 ASP A 468 ASN A 495
1 28  
Start residue of secondary structure not found: HELIX 5 5 GLU A 499 ASN A 526
1 28  
55 messages similar to the above omitted  
  
Chain information for c7_pl416_apply_ncs_6_INPUT_C9_symm_0001_s.pdb #1  
---  
Chain | Description  
G | No description available  
  

> open
> /Users/mac/Documents/Projects/symetry/c7/c7_pl416_model/c7_pl416_P263_J1478_008_volume_map_sharp_3.57.mrc

Opened c7_pl416_P263_J1478_008_volume_map_sharp_3.57.mrc as #2, grid size
256,256,256, pixel 1.08, shown at level 0.257, step 1, values float32  

> ui tool show ISOLDE

/private/var/folders/84/yp82d91d5jvdwmx6kd1td9640000gn/T/AppTranslocation/A0A94592-2F19-46B9-8EE6-D3AC8447FB69/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:411: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'AGBNP3':  
/private/var/folders/84/yp82d91d5jvdwmx6kd1td9640000gn/T/AppTranslocation/A0A94592-2F19-46B9-8EE6-D3AC8447FB69/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:433: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'GVolSA':  
/private/var/folders/84/yp82d91d5jvdwmx6kd1td9640000gn/T/AppTranslocation/A0A94592-2F19-46B9-8EE6-D3AC8447FB69/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:440: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'AGBNP':  

> set selectionWidth 4

Chain information for c7_pl416_apply_ncs_6_INPUT_C9_symm_0001_s.pdb  
---  
Chain | Description  
1.2/G | No description available  
  
Done loading forcefield  
Opened c7_pl416_P263_J1478_008_volume_map_sharp_3.57.mrc as #1.1.1.1, grid
size 256,256,256, pixel 1.08, shown at step 1, values float32  

> select clear

Populating font family aliases took 1091 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: stopped sim  

> select clear

ISOLDE: started sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
reverting to start  
ISOLDE: stopped sim  

> select clear

> select clear

> select clear

> select clear

> select clear

ISOLDE: started sim  
reverting to start  
ISOLDE: stopped sim  

> undo

> undo

> select clear

> close #1

Window position QRect(1829,1237 719x20) outside any known screen, using
primary screen  

> open
> /Users/mac/Documents/Projects/symetry/c7/c7_pl416_model/c7_pl416_P263_J1478_008_volume_map_sharp_3.57.mrc
> format mrc

Opened c7_pl416_P263_J1478_008_volume_map_sharp_3.57.mrc as #1, grid size
256,256,256, pixel 1.08, shown at level 0.257, step 1, values float32  

> open
> /Users/mac/Documents/Projects/symetry/c7/c7_pl416_model/ApplyNCS_9/c7_pl416_apply_ncs_6_INPUT_C9_symm_0001_s.pdb

Summary of feedback from opening
/Users/mac/Documents/Projects/symetry/c7/c7_pl416_model/ApplyNCS_9/c7_pl416_apply_ncs_6_INPUT_C9_symm_0001_s.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 375
ASN A 402 1 28  
Start residue of secondary structure not found: HELIX 2 2 GLU A 406 ASN A 433
1 28  
Start residue of secondary structure not found: HELIX 3 3 GLU A 437 ASN A 464
1 28  
Start residue of secondary structure not found: HELIX 4 4 ASP A 468 ASN A 495
1 28  
Start residue of secondary structure not found: HELIX 5 5 GLU A 499 ASN A 526
1 28  
55 messages similar to the above omitted  
  
Chain information for c7_pl416_apply_ncs_6_INPUT_C9_symm_0001_s.pdb #2  
---  
Chain | Description  
G | No description available  
  
Chain information for c7_pl416_apply_ncs_6_INPUT_C9_symm_0001_s.pdb  
---  
Chain | Description  
2.2/G | No description available  
  
Opened c7_pl416_P263_J1478_008_volume_map_sharp_3.57.mrc as #2.1.1.1, grid
size 256,256,256, pixel 1.08, shown at step 1, values float32  
Traceback (most recent call last):  
File "/Users/mac/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/clashes.py", line 223, in
_show_selected_clash  
get_stepper(residues[0].structure).step_to(residues[0])  
File
"/private/var/folders/84/yp82d91d5jvdwmx6kd1td9640000gn/T/AppTranslocation/A0A94592-2F19-46B9-8EE6-D3AC8447FB69/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
IndexError: index 0 is out of bounds for axis 0 with size 0  
  
IndexError: index 0 is out of bounds for axis 0 with size 0  
  
File
"/private/var/folders/84/yp82d91d5jvdwmx6kd1td9640000gn/T/AppTranslocation/A0A94592-2F19-46B9-8EE6-D3AC8447FB69/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/mac/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/clashes.py", line 223, in
_show_selected_clash  
get_stepper(residues[0].structure).step_to(residues[0])  
File
"/private/var/folders/84/yp82d91d5jvdwmx6kd1td9640000gn/T/AppTranslocation/A0A94592-2F19-46B9-8EE6-D3AC8447FB69/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
IndexError: index 0 is out of bounds for axis 0 with size 0  
  
IndexError: index 0 is out of bounds for axis 0 with size 0  
  
File
"/private/var/folders/84/yp82d91d5jvdwmx6kd1td9640000gn/T/AppTranslocation/A0A94592-2F19-46B9-8EE6-D3AC8447FB69/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
  
See log for complete Python traceback.  
  

> select clear

> select clear

> select clear

Traceback (most recent call last):  
File "/Users/mac/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/clashes.py", line 223, in
_show_selected_clash  
get_stepper(residues[0].structure).step_to(residues[0])  
File
"/private/var/folders/84/yp82d91d5jvdwmx6kd1td9640000gn/T/AppTranslocation/A0A94592-2F19-46B9-8EE6-D3AC8447FB69/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
IndexError: index 0 is out of bounds for axis 0 with size 0  
  
IndexError: index 0 is out of bounds for axis 0 with size 0  
  
File
"/private/var/folders/84/yp82d91d5jvdwmx6kd1td9640000gn/T/AppTranslocation/A0A94592-2F19-46B9-8EE6-D3AC8447FB69/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.4.5
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 429.120.4.0.0
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 16 days 7:06

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2421D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: J26VQ33     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: Thunderbolt/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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 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 _show_selected_clash: 'residues' is empty

comment:2 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

If I recall correctly, the clashes table wasn't clearing itself when the working model was deleted, and clicking on one of the zombie entries would cause this clash. Fixed by the new ISOLDE GUI.

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