Opened 7 months ago

Last modified 7 months ago

#17293 assigned defect

DiffFit: 'NoneType' object has no attribute 'step'

Reported by: thachang@… Owned by: Roden Deng Luo
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:        Linux-6.8.0-52-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/prasadlab/anish/P15/W3T4/cryosparc_P15_J77_006_volume_T4map.mrc

Opened cryosparc_P15_J77_006_volume_T4map.mrc as #1, grid size 980,980,980,
pixel 1.08, shown at step 1, values float32  

> volume #1 region 0,0,0,979,979,979 step 4

[Repeated 1 time(s)]

> open
> /home/prasadlab/anish/P15/W3/7mryRelative_real_space_refined_007-coot-4.pdb

Chain information for 7mryRelative_real_space_refined_007-coot-4.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #!1 models

> open /home/prasadlab/anish/P15/W3/T3vlp_with_map.pdb

Summary of feedback from opening
/home/prasadlab/anish/P15/W3/T3vlp_with_map.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 10 SER A 12 1 3  
Start residue of secondary structure not found: HELIX 9 9 ALA B 635 ALA B 638
1 4  
Start residue of secondary structure not found: HELIX 10 10 PRO B 650 ASN B
654 1 5  
Start residue of secondary structure not found: HELIX 11 11 PRO B 683 LEU B
685 1 3  
Start residue of secondary structure not found: HELIX 12 12 PRO B 687 HIS B
691 1 5  
3475 messages similar to the above omitted  
  
Chain information for T3vlp_with_map.pdb  
---  
Chain | Description  
3.1/A | No description available  
3.2/A | No description available  
3.1/B | No description available  
3.2/B 3.2/C | No description available  
3.1/C | No description available  
  

> close

> open /home/prasadlab/anish/P15/W3T4/cryosparc_P15_J77_006_volume_T4map.mrc

Opened cryosparc_P15_J77_006_volume_T4map.mrc as #1, grid size 980,980,980,
pixel 1.08, shown at step 1, values float32  

> volume #1 region 0,0,0,979,979,979 step 4

[Repeated 1 time(s)]

> volume showOutlineBox true

> ui mousemode right "crop volume"

> volume #1 region 0,0,225,979,979,979

> volume #1 region 0,231,225,979,979,979

> volume #1 region 0,231,225,979,754,979

> volume #1 region 0,231,225,979,754,752

> volume #1 region 0,231,225,734,754,752

> volume #1 region 246,231,225,734,754,752

> volume #1 region 246,231,225,734,754,727

> volume #1 region 246,231,225,734,754,721

> volume #1 region 246,231,255,734,754,721

> volume #1 region 246,254,255,734,754,721

> volume #1 region 246,254,255,734,718,721

> volume #1 region 257,254,255,734,718,721

> volume #1 region 257,254,255,722,718,721

> volume #1 level 0.1

> volume #1 change image level -0.02595,0 level 0.1857,0.8 level 0.4778,1

> volume showOutlineBox false

> ui mousemode right "map eraser"

> volume erase #1 center 697,560.29,581.19 radius 82.656 outside true

Opened cryosparc_P15_J77_006_volume_T4map.mrc copy as #3, grid size
466,465,467, pixel 1.08, shown at step 1, values float32  

> volume #1 step 1

> volume #3 color #ffffb2

> hide #2 models

> open /home/prasadlab/anish/P15/W3T4/6ouu.pdb

6ouu.pdb title:  
Symmetric reconstruction of human norovirus gii.4 minerva strain VLP In T=4
symmetry [more info...]  
  
Chain information for 6ouu.pdb #4  
---  
Chain | Description | UniProt  
A B C D | major capsid protein | R4I3T2_9CALI 1-540  
  

> select #4

14982 atoms, 15449 bonds, 1 pseudobond, 1935 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,10.169,0,1,0,7.2616,0,0,1,-0.49523

> view matrix models
> #4,0.81193,0.49865,-0.3035,33.216,-0.2611,-0.15481,-0.95282,1240,-0.52211,0.85287,0.004505,408.98

> view matrix models
> #4,0.88681,-0.42129,0.18995,138.08,0.045009,-0.33035,-0.94279,1197,0.45993,0.84462,-0.274,198.02

> view matrix models
> #4,0.96266,0.10613,-0.24904,126.85,-0.0059581,-0.91143,-0.41142,1167.4,-0.27065,0.39754,-0.87676,1065.3

> view matrix models
> #4,0.37808,0.87791,0.29382,-341.78,0.85426,-0.45315,0.25475,205.2,0.35679,0.15469,-0.92129,961.51

> view matrix models
> #4,-0.7781,0.23546,0.58235,239.82,0.61726,0.11474,0.77835,-291.35,0.11645,0.96509,-0.23462,251.56

> view matrix models
> #4,-0.82817,0.23215,0.51014,305.2,0.42542,-0.3322,0.84182,-43.043,0.3649,0.91419,0.17636,-73.175

> view matrix models
> #4,-0.40237,0.56187,0.72277,-148.2,0.65105,-0.37941,0.6574,3.6406,0.6436,0.73508,-0.21314,140.67

> view matrix models
> #4,-0.50491,0.34885,0.78954,-47.836,0.82537,-0.072576,0.5599,-150.56,0.25262,0.93437,-0.25129,222.91

> view matrix models
> #4,-0.57459,0.26765,0.77344,27.835,0.78307,-0.095021,0.61463,-156.8,0.238,0.95882,-0.15499,158.14

> view matrix models
> #4,-0.57459,0.26765,0.77344,329.07,0.78307,-0.095021,0.61463,-39.153,0.238,0.95882,-0.15499,192.83

> view matrix models
> #4,-0.57459,0.26765,0.77344,358.94,0.78307,-0.095021,0.61463,-69.717,0.238,0.95882,-0.15499,130.83

> view matrix models
> #4,-0.61832,-0.0037971,0.78592,497.14,0.77023,-0.20178,0.605,-8.1795,0.15629,0.97942,0.12769,-19.804

> view matrix models
> #4,-0.61832,-0.0037971,0.78592,479.25,0.77023,-0.20178,0.605,-8.7975,0.15629,0.97942,0.12769,-26.275

> view matrix models
> #4,-0.57966,0.21443,0.78614,360.5,0.23849,-0.87787,0.4153,636.34,0.77918,0.42822,0.45773,-211.21

> view matrix models
> #4,-0.57659,0.22251,0.78615,355.46,0.23572,-0.87598,0.42082,633.15,0.78229,0.42796,0.45263,-209.19

> view matrix models
> #4,-0.57659,0.22251,0.78615,354.13,0.23572,-0.87598,0.42082,640.91,0.78229,0.42796,0.45263,-207.52

> ui tool show DiffFit

loading settings...  
Traceback (most recent call last):  
File "/home/prasadlab/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/difffit/tool.py", line 435, in <lambda>  
button_fit.clicked.connect(lambda: self.single_fit_button_clicked())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/prasadlab/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/difffit/tool.py", line 1703, in single_fit_button_clicked  
mol_vol = molecule_map(self.session, mol.atoms, self._single_fit_res.value(),
grid_spacing=self.fit_vol.data.step[0])  
^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'step'  
  
AttributeError: 'NoneType' object has no attribute 'step'  
  
File "/home/prasadlab/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/chimerax/difffit/tool.py", line 1703, in single_fit_button_clicked  
mol_vol = molecule_map(self.session, mol.atoms, self._single_fit_res.value(),
grid_spacing=self.fit_vol.data.step[0])  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA RTX A6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 128 AMD Ryzen Threadripper PRO 3995WX 64-Cores
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           251Gi        24Gi       171Gi        84Mi        54Gi       224Gi
	Swap:            9Gi       1.2Gi       8.8Gi

Graphics:
	41:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A6000] [10de:2230] (rev a1)	
	Subsystem: NVIDIA Corporation GA102GL [RTX A6000] [10de:1459]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    biopython: 1.83
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    DiffFit: 0.7.0
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    fsspec: 2025.2.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    mpmath: 1.3.0
    mrcfile: 1.5.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    nvidia-cublas-cu12: 12.1.3.1
    nvidia-cuda-cupti-cu12: 12.1.105
    nvidia-cuda-nvrtc-cu12: 12.1.105
    nvidia-cuda-runtime-cu12: 12.1.105
    nvidia-cudnn-cu12: 8.9.2.26
    nvidia-cufft-cu12: 11.0.2.54
    nvidia-curand-cu12: 10.3.2.106
    nvidia-cusolver-cu12: 11.4.5.107
    nvidia-cusparse-cu12: 12.1.0.106
    nvidia-nccl-cu12: 2.19.3
    nvidia-nvjitlink-cu12: 12.8.61
    nvidia-nvtx-cu12: 12.1.105
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    sympy: 1.13.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    torch: 2.2.1
    tornado: 6.4.2
    traitlets: 5.14.3
    triton: 2.2.0
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (1)

comment:1 by Eric Pettersen, 7 months ago

Component: Unassigned → Third Party
Owner: set to Roden Deng Luo
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → DiffFit: 'NoneType' object has no attribute 'step'
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