ISOLDE: 'NoneType' object has no attribute 'sim_construct'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\Users\\\wucang\\\Desktop\\\MODEL\\\AFP\\\afp_md_real_space_refined_067-coot-6.pdb

Chain information for afp_md_real_space_refined_067-coot-6.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open E:/Download/cryosparc_P23_J1008_009_volume_map_sharp.mrc

Opened cryosparc_P23_J1008_009_volume_map_sharp.mrc as #2, grid size
192,192,192, pixel 1.05, shown at level 0.0913, step 1, values float32  

> volume #2 level 0.2645

> fitmap #1 inMap #2

Fit molecule afp_md_real_space_refined_067-coot-6.pdb (#1) to map
cryosparc_P23_J1008_009_volume_map_sharp.mrc (#2) using 4763 atoms  
average map value = 0.4897, steps = 52  
shifted from previous position = 0.268  
rotated from previous position = 1.42 degrees  
atoms outside contour = 1363, contour level = 0.26452  
  
Position of afp_md_real_space_refined_067-coot-6.pdb (#1) relative to
cryosparc_P23_J1008_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99973574 0.00943083 0.02096467 -3.13925804  
-0.00962342 0.99991225 0.00910442 0.23512341  
-0.02087697 -0.00930377 0.99973876 2.89876509  
Axis -0.37170081 0.84487212 -0.38474615  
Axis point 141.62080814 0.00000000 147.08909935  
Rotation angle (degrees) 1.41890957  
Shift along axis 0.25022526  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 25 residues in model #1 to IUPAC-IUB
standards.  
Chain information for afp_md_real_space_refined_067-coot-6.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> addh #1.2

Summary of feedback from adding hydrogens to
afp_md_real_space_refined_067-coot-6.pdb #1.2  
---  
notes | No usable SEQRES records for afp_md_real_space_refined_067-coot-6.pdb
(#1.2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A ARG 19  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A VAL 609  
Chain-final residues that are not actual C termini:  
465 hydrogen bonds  
4725 hydrogens added  
  
Loading residue template for PLM from internal database  

> isolde tutorial

> clipper associate #2 toModel #1

Opened cryosparc_P23_J1008_009_volume_map_sharp.mrc as #1.1.1.1, grid size
192,192,192, pixel 1.05, shown at step 1, values float32  

> isolde start

[Repeated 1 time(s)]

> set bgColor white

> isolde restrain ligands #1

> select #1

9488 atoms, 9586 bonds, 599 residues, 15 models selected  

> isolde sim start sel

ISOLDE: started sim  

> ui tool show "Ramachandran Plot"

> volume #1.1.1.1 level 0.2466

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #1.1.1.1 level 0.1437

> volume #1.1.1.1 level 0.1166

> isolde sim stop

> set selectionWidth 4

No simulation is currently running!  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 637, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Users\wucang\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\tugging.py", line 124, in mouse_down  
pa = self._pick_atoms(pick)  
File "C:\Users\wucang\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\tugging.py", line 154, in _pick_atoms  
if self.atoms.index(a) != -1:  
File "C:\Users\wucang\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\tugging.py", line 55, in atoms  
return self.session.isolde.sim_manager.sim_construct.mobile_atoms  
AttributeError: 'NoneType' object has no attribute 'sim_construct'  
  
AttributeError: 'NoneType' object has no attribute 'sim_construct'  
  
File "C:\Users\wucang\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\tugging.py", line 55, in atoms  
return self.session.isolde.sim_manager.sim_construct.mobile_atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 637, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Users\wucang\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\tugging.py", line 124, in mouse_down  
pa = self._pick_atoms(pick)  
File "C:\Users\wucang\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\tugging.py", line 154, in _pick_atoms  
if self.atoms.index(a) != -1:  
File "C:\Users\wucang\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\tugging.py", line 55, in atoms  
return self.session.isolde.sim_manager.sim_construct.mobile_atoms  
AttributeError: 'NoneType' object has no attribute 'sim_construct'  
  
AttributeError: 'NoneType' object has no attribute 'sim_construct'  
  
File "C:\Users\wucang\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\tugging.py", line 55, in atoms  
return self.session.isolde.sim_manager.sim_construct.mobile_atoms  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 536.40
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: LENOVO
Model: 82JQ
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 68,564,348,928
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics         
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-ISOLDE: 1.5
    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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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-StarMap: 1.1.70
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
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    entrypoints: 0.4
    executing: 1.2.0
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    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
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    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

[Tristan Croll]

That took a little puzzling to figure out what happened. The user closed
ISOLDE while a simulation was actively running... turns out that leaves the
simulation endlessly running, detached from all the controls - reopening
ISOLDE creates an entirely new ISOLDE object. Will adjust to make sure that
closing ISOLDE kills and cleans up any running simulation.

On Tue, Jul 11, 2023 at 5:21 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>

[Tristan Croll]

Ah - I see what's happened. For some unfathomable reason, on closing the
GUI panel I had it cleaning up all ISOLDE's callbacks *before* calling
`stop_sim()`... ugh.

On Wed, Jul 12, 2023 at 2:33 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>

[Tristan Croll]

Urgh - worse than that. The cleanup method for the core ISOLDE object
wasn't actually being called *at all* - an oversight when rebuilding the
GUI. Fixed now - but at the moment I can't log into Trac at all (even on
the Linux machine that previously worked) so can't close the ticket.

On Wed, Jul 12, 2023 at 2:59 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>

[Eric Pettersen]

Tristan can't log into Trac (#9136), so closing this on his behalf.