SEQCROW: model.session is None while applying preset to morph

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-6.8.0-59-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Just got this traceback from SEQCROW, seemingly entirely at random. Generated a morph, closed it, trimmed a few errant residues off one of the input models and generated a new morph, which triggered the traceback.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
Running command "isolde shorthand"  

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Running command "open 9f19_isolde.cif"  

> open 9f19_isolde.cif

Summary of feedback from opening 9f19_isolde.cif  
---  
warnings | Unknown polymer entity '1' on line 140  
Unknown polymer entity '2' on line 4559  
Atom H is not in the residue template for LEU /A:66  
Atom H12 is not in the residue template for A1H8X /A:601  
Atom H is not in the residue template for LYS /B:64  
Atom H12 is not in the residue template for A1H8X /*B:601  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 9f19_isolde.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Drag select of 184 atoms, 98 residues, 1 pseudobonds, 171 bonds  
Running command "select up"  

> select up

1681 atoms, 1695 bonds, 1 pseudobond, 103 residues, 2 models selected  
Running command "select up"  

> select up

1755 atoms, 1773 bonds, 1 pseudobond, 103 residues, 2 models selected  
Running command "select up"  

> select up

2462 atoms, 2491 bonds, 1 pseudobond, 152 residues, 2 models selected  
Running command "select up"  

> select up

4324 atoms, 4382 bonds, 1 pseudobond, 271 residues, 2 models selected  

> delete sel

> alphafold match #1

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold A0A2K6RVV2 from
https://alphafold.ebi.ac.uk/files/AF-A0A2K6RVV2-F1-model_v4.cif  
1 AlphaFold model found using sequence similarity searches: A0A2K6RVV2 (chain
A)  
AlphaFold prediction matching 9f19_isolde.cif  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
A | A0A2K6RVV2 | A0A2K6RVV2_RHIRO | 10.56 | 437 | 274 | 86   
  
Opened 1 AlphaFold model  
Running command "close #2"  

> close #2

> alphafold fetch Q70CQ3

Chain information for AlphaFold Q70CQ3 #2  
---  
Chain | Description | UniProt  
A | Ubiquitin carboxyl-terminal hydrolase 30 | UBP30_HUMAN 1-517  
  
Color AlphaFold Q70CQ3 by residue attribute pLDDT_score  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9f19_isolde.cif, chain A (#1) with AlphaFold Q70CQ3, chain A (#2),
sequence alignment score = 990.2  
RMSD between 212 pruned atom pairs is 0.725 angstroms; (across all 274 pairs:
4.046)  
  

> cbc

> iniot

Unknown command: clipper iniot  

> clipper init

Running command "cofr center showPivot t"  

> cofr centerOfView showPivot true

Running command "camera ortho"  

> camera ortho

Running command "lighting simple"  

> lighting simple

> morph #2,1 frames 120

Computed 121 frame morph #3  
Running command "coordset #3 1,121"  

> coordset #3 1,121

Running command "close #3"  

> close #3

Running command "show #!1 models"  

> show #!1 models

Running command "show #2 models"  

> show #2 models

> delete #2:358-430

> morph #2,1 frames 120

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/tcroll/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/SEQCROW/managers/filereader_manager.py", line 58, in apply_preset  
if model.session.ui.is_gui:  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'ui'  
  
Error processing trigger "add models":  
AttributeError: 'NoneType' object has no attribute 'ui'  
  
File "/home/tcroll/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/SEQCROW/managers/filereader_manager.py", line 58, in apply_preset  
if model.session.ui.is_gui:  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Computed 121 frame morph #3  
Running command "coordset #3 1,121"  

> coordset #3 1,121




OpenGL version: 3.3.0 NVIDIA 535.230.02
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.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=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        11Gi       6.8Gi       703Mi        12Gi        18Gi
	Swap:          2.0Gi       1.5Gi       538Mi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)	
	Subsystem: Dell GA104 [GeForce RTX 3070 Lite Hash Rate] [1028:c903]	
	Kernel driver in use: nvidia

Installed Packages:
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    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
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    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
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    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
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    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
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    ChimeraX-CellPack: 1.0
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    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    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-ISOLDE: 1.9
    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: 1.2
    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
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    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
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    executing: 2.1.0
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    imagecodecs: 2024.6.1
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    inflect: 7.3.1
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    Pygments: 2.18.0
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    pynrrd: 1.0.0
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    rdkit: 2024.9.6
    requests: 2.32.3
    scipy: 1.14.0
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    Send2Trash: 1.8.3
    SEQCROW: 1.8.17
    setuptools: 72.1.0
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    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
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    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

[Eric Pettersen]

Reported by Tristan Croll

[Tom Goddard]

Tony, the morph command is creating the new morph atomic structure model, and then computing the new coordinates, and then adding it to the session. I'm guessing your code is getting a trigger callback when the model is created, but it has not yet been added to the session.

[Tony Schaefer]

Tristan,

Thanks for reporting this

Tom,

I think you're right about what's causing this. It seems similar to a bug I
had in OpenCommands a while back.

This might be a busy week, but I'll see if I can get a patch out soon.

Best,

Tony

On Fri, Jun 6, 2025 at 1:35 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>