Drawing volume: object of type 'NoneType' has no len()

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open E:\\\实验室\\\其它\\\14-课题整理\\\1-model\\\23.7.28-UDP-
> Gal\\\cryosparc_P21_J1359_007_volume_map_sharp.mrc

Opened cryosparc_P21_J1359_007_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 1.1, shown at level 0.148, step 2, values float32  

> volume #1 step 1

> open E:/实验室/其它/14-课题整理/1-model/model更新/J1170(+UDP-gal)/PLO-
> COL_J1170-ABUV.pdb

Chain information for PLO-COL_J1170-ABUV.pdb #2  
---  
Chain | Description  
A B | No description available  
U V | No description available  
  

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule PLO-COL_J1170-ABUV.pdb (#2) to map
cryosparc_P21_J1359_007_volume_map_sharp.mrc (#1) using 20982 atoms  
average map value = 0.7665, steps = 60  
shifted from previous position = 0.2  
rotated from previous position = 0.156 degrees  
atoms outside contour = 1181, contour level = 0.14786  
  
Position of PLO-COL_J1170-ABUV.pdb (#2) relative to
cryosparc_P21_J1359_007_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999932 -0.00002366 0.00116401 -0.29423223  
0.00002079 0.99999696 0.00246422 -0.53838341  
-0.00116406 -0.00246419 0.99999629 0.96742075  
Axis -0.90416399 0.42710770 0.00815487  
Axis point 0.00000000 392.10477109 226.58580708  
Rotation angle (degrees) 0.15615376  
Shift along axis 0.04397567  
  

> volume #1 color #1d40b2

> volume #1 color #482db2

> transparency #7 30

> transparency #1 30

> set bgColor white

> color #1 #4c37b2ff models

> transparency #1 30

> volume #1 level 0.4463

> volume #1 level 0.3468

> volume #1 level 0.322

> open E:/实验室/其它/14-课题整理/1-model/model更新/Apo/PLOD-COL_012-coot-0.pdb

Summary of feedback from opening E:/实验室/其它/14-课题整理/1-model/model更新/Apo/PLOD-
COL_012-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 87 87 LYS V
593 GLU V 603 1 11  
Start residue of secondary structure not found: HELIX 129 129 LYS W 593 GLU W
603 1 11  
Start residue of secondary structure not found: HELIX 148 148 LYS X 593 GLU X
603 1 11  
  
Chain information for PLOD-COL_012-coot-0.pdb #3  
---  
Chain | Description  
A B C | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
  

> hide #!2 models

> show #!3 cartoons

> hide #!3 atoms

> volume zone #1 nearAtoms #3 range 1.8 newMap true

Opened cryosparc_P21_J1359_007_volume_map_sharp.mrc zone as #4, grid size
384,384,384, pixel 1.1, shown at step 1, values float32  

> close #4

> ui tool show "Fit in Map"

> fitmap #3 inMap #1

Fit molecule PLOD-COL_012-coot-0.pdb (#3) to map
cryosparc_P21_J1359_007_volume_map_sharp.mrc (#1) using 35111 atoms  
average map value = 0.537, steps = 88  
shifted from previous position = 1.63  
rotated from previous position = 2.92 degrees  
atoms outside contour = 17364, contour level = 0.32195  
  
Position of PLOD-COL_012-coot-0.pdb (#3) relative to
cryosparc_P21_J1359_007_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99922491 -0.03592968 -0.01608193 11.48059262  
0.03539048 0.99884031 -0.03264282 0.32269946  
0.01723612 0.03204837 0.99933769 -11.78278494  
Axis 0.63491098 -0.32699963 0.69997092  
Axis point 11.79087749 338.07656652 0.00000000  
Rotation angle (degrees) 2.92020286  
Shift along axis -1.06397507  
  

> show #!2 models

> show #!1 models

> volume zone #1 nearAtoms #3 range 1.8 newMap true

Opened cryosparc_P21_J1359_007_volume_map_sharp.mrc zone as #4, grid size
384,384,384, pixel 1.1, shown at step 1, values float32  

> hide #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!2 models

> show #!1 models

> volume subtract #1 #4 modelId #5

Opened volume difference as #5, grid size 384,384,384, pixel 1.1, shown at
step 1, values float32  

> hide #!2 models

> show #!2 models

> hide #!3 models

> volume #1 level 0.3476

> hide #!1 models

> hide #!5 models

> show #!5 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> select ::name="AKG"

20 atoms, 18 bonds, 2 residues, 1 model selected  

> hide #!5 models

> hide #!2 models

> open
> C:/Users/Administrator/Downloads/cryosparc_P21_J1377_008_volume_map_sharp.mrc

Opened cryosparc_P21_J1377_008_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 1.2, shown at level 0.139, step 2, values float32  

> close #5

[Repeated 1 time(s)]Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\map\volume_viewer.py", line
2295, in show_cb  
v.display = show  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py", line 729, in
_set_display  
Model.display.fset(self, display)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\models.py", line 324, in
_set_display  
Drawing.set_display(self, display)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
380, in set_display  
dp = self.display_positions  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
394, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
394, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\map\volume_viewer.py", line
2295, in show_cb  
v.display = show  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py", line 729, in
_set_display  
Model.display.fset(self, display)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\models.py", line 324, in
_set_display  
Drawing.set_display(self, display)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
380, in set_display  
dp = self.display_positions  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
394, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
394, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\map\volume_viewer.py", line
2295, in show_cb  
v.display = show  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py", line 729, in
_set_display  
Model.display.fset(self, display)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\models.py", line 324, in
_set_display  
Drawing.set_display(self, display)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
380, in set_display  
dp = self.display_positions  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
394, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
394, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\map\volume_viewer.py", line
2126, in close_map_cb  
log_equivalent_command(v.session, 'close #%s' % v.id_string)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\logging.py",
line 29, in log_equivalent_command  
command.run(command_text, log_only=True)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2853, in run  
prev_annos = self._process_positional_arguments()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2629, in _process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2488, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
1265, in parse  
models = aspec.evaluate(session).models  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\atomspec.py",
line 1067, in evaluate  
models = session.models.list(**kw)  
AttributeError: 'NoneType' object has no attribute 'models'  
  
AttributeError: 'NoneType' object has no attribute 'models'  
  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\atomspec.py",
line 1067, in evaluate  
models = session.models.list(**kw)  
  
See log for complete Python traceback.  
  

> select add #2

20982 atoms, 21569 bonds, 10 pseudobonds, 2558 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select add #2

20982 atoms, 21569 bonds, 10 pseudobonds, 2558 residues, 3 models selected  

> show #!2 models

> select subtract #2

Nothing selected  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\map\volume_viewer.py", line
2295, in show_cb  
v.display = show  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py", line 729, in
_set_display  
Model.display.fset(self, display)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\models.py", line 324, in
_set_display  
Drawing.set_display(self, display)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
380, in set_display  
dp = self.display_positions  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
394, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\graphics\drawing.py", line
394, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 536.99
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Acer
Model: Predator PHN16-71
OS: Microsoft Windows 10 专业版 (Build 19044)
Memory: 16,886,128,640
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i5-13500HX
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
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[Tom Goddard]

Yikes. The "volume subtract #1 #4 modelId #5" created a model id #5 and then the next map opened from a file also created model #5. The Models code does some caching of the next available model id that is broken if a model is added with a specified id.

[Tom Goddard]

Fixed.

Any code that added a model with the id already set did not end up updating the highest used model id used by session.models which could cause a subsequently opened model to reuse an already used id. That would surely cause havoc. Probably we have seen this bug reported many times but did not figure it out. Fixed now by reseting the highest unused id if a model is added with a specified id.