Opened 9 months ago

Last modified 9 months ago

#16620 assigned defect

Installing SEQCROW nukes multiple unrelated commands

Reported by: Tristan Croll Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Tony Schaefer
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.8.0-51-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Just installed SEQCROW from the ToolShed, and somehow the "match" command is now borked... if I type "match #5 to #1" on the command line, the "match" is totally ignored leading to a "Missing command" error.

Problem *seems* to be resolved in a fresh session, but still reporting it because it's just plain weird.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> 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  

> open 4j1p structureFactors true

Summary of feedback from opening 4j1p fetched from pdb  
---  
notes | Fetching compressed mmCIF 4j1p from http://files.rcsb.org/download/4j1p.cif  
Fetching CCD 1K0 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/1K0/1K0.cif  
Fetching compressed 4j1p structure factors from
http://files.rcsb.org/download/4j1p-sf.cif  
Resolution: 1.0790460686274326  
Launching live xmap mgr took 0.828131914138794 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 70,72,70, pixel
0.355,0.346,0.351, shown at level 1.21, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 70,72,70, pixel
0.355,0.346,0.351, shown at level -0.225,0.225, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_27 as #1.1.1.4, grid size 70,72,70, pixel
0.355,0.346,0.351, shown at level 0.23, step 1, values float32  
4j1p title:  
X-ray crystal structure of bromodomain 2 of human brd2 in complex with rvx208
to 1.08 A resolution [more info...]  
  
Chain information for 4j1p  
---  
Chain | Description | UniProt  
1.2/A | Bromodomain containing 2, isoform CRA_a | Q658Y7_HUMAN 344-455  
  
Non-standard residues in 4j1p #1.2  
---  
1K0 —
2-[4-(2-hydroxyethoxy)-3,5-dimethylphenyl]-5,7-dimethoxyquinazolin-4(3H)-one  
EDO — 1,2-ethanediol (ethylene glycol)  
  
77 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> view :1K0

> addh

Summary of feedback from adding hydrogens to 4j1p #1.2  
---  
notes | Termini for 4j1p (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A SER 342  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASP 455  
Chain-final residues that are not actual C termini:  
845 hydrogen bonds  
1460 hydrogens added  
  

> alphafold fetch Q15059

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold Q15059 from
https://alphafold.ebi.ac.uk/files/AF-Q15059-F1-model_v4.cif  
Chain information for AlphaFold Q15059 #2  
---  
Chain | Description | UniProt  
A | Bromodomain-containing protein 3 | BRD3_HUMAN 1-726  
  
Color AlphaFold Q15059 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 4j1p, chain A (#1.2) with AlphaFold Q15059, chain A (#2), sequence
alignment score = 508.2  
RMSD between 109 pruned atom pairs is 0.497 angstroms; (across all 114 pairs:
2.062)  
  

> show #2

> color byhetero

> color #2 orange

> color byhetero

> rename #2 "AlphaFold Q15059 brd3"

> select clear

> delete #2&~:305-419

> alphafold fetch O60885

Fetching compressed AlphaFold O60885 from
https://alphafold.ebi.ac.uk/files/AF-O60885-F1-model_v4.cif  
Chain information for AlphaFold O60885 #3  
---  
Chain | Description | UniProt  
A | Bromodomain-containing protein 4 | BRD4_HUMAN 1-1362  
  
Color AlphaFold O60885 by residue attribute pLDDT_score  

> matchmaker #3 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 4j1p, chain A (#1.2) with AlphaFold O60885, chain A (#3), sequence
alignment score = 499.8  
RMSD between 108 pruned atom pairs is 0.537 angstroms; (across all 114 pairs:
1.883)  
  

> color #3 brown

> color byhetero

> show #3

> delete #3&~:348--461

> alphafold fetch O60885

Chain information for AlphaFold O60885 #3  
---  
Chain | Description | UniProt  
A | Bromodomain-containing protein 4 | BRD4_HUMAN 1-1362  
  
Color AlphaFold O60885 by residue attribute pLDDT_score  

> matchmaker #3 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 4j1p, chain A (#1.2) with AlphaFold O60885, chain A (#3), sequence
alignment score = 499.8  
RMSD between 108 pruned atom pairs is 0.537 angstroms; (across all 114 pairs:
1.883)  
  

> color #3 brown

> color byhetero

> show #3

> delete #3&~:348-461

> select clear

> hide :HOH

> hide #!1.1 models

> toolshed show

Downloading bundle SEQCROW-1.8.17-py3-none-any.whl  
Installed SEQCROW (1.8.17)  

> ui tool show "2D Builder"

Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

> undo

getting structure  

> lighting simple

> graphics silhouettes false

> move cofr #4

> select #4

47 atoms, 50 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.31072,0.9045,-0.29211,9.9443,-0.38635,-0.1606,-0.90826,22.926,-0.86844,0.39508,0.29955,-4.6693

> view matrix models
> #4,0.51622,0.75306,0.40794,4.4173,0.30952,0.28009,-0.90871,21.868,-0.79857,0.59535,-0.0885,2.0216

> view matrix models
> #4,0.3397,0.5533,0.76057,8.9485,0.4504,0.6142,-0.64799,20.191,-0.82568,0.56268,-0.040568,2.313

> view matrix models
> #4,0.65424,0.64515,0.39466,9.869,-0.16907,0.6334,-0.75513,21.175,-0.73715,0.42731,0.52347,1.119

> view matrix models
> #4,-0.0082595,0.96978,0.24385,9.7563,-0.025408,0.24358,-0.96955,23.22,-0.99964,-0.014204,0.022629,-0.77924

> select subtract #4

Nothing selected  

> alphafold fetch P25440

Fetching compressed AlphaFold P25440 from
https://alphafold.ebi.ac.uk/files/AF-P25440-F1-model_v4.cif  
Chain information for AlphaFold P25440 #5  
---  
Chain | Description | UniProt  
A | Bromodomain-containing protein 2 | BRD2_HUMAN 1-801  
  
Color AlphaFold P25440 by residue attribute pLDDT_score  

>

Missing command  

>

Missing command  

>

Missing command  

> select clear

> view #1

>

Missing command  

> alias list

> usage match

  

> toolshed show

>

Missing command  




OpenGL version: 3.3.0 NVIDIA 535.216.03
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        14Gi       8.1Gi       806Mi       8.3Gi        15Gi
	Swap:          2.0Gi          0B       2.0Gi

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:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    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-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
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    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
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    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
    more-itertools: 10.3.0
    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
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    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
    platformdirs: 4.2.2
    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
    Send2Trash: 1.8.3
    SEQCROW: 1.8.17
    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
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    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: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (4)

comment:1 by Tristan Croll, 9 months ago

Platform: → all
Project: → ChimeraX

Doing a little digging while the messed-up session is still open... a bunch (but still a fairly small subset) of commands seem to have been messed up:

from chimerax.core.commands.cli import _command_info
cmds = _command_info.commands
for key, cmd in cmds.subcommands.items():
    if cmd.cmd_desc is None:
        print(key)

toolshed
devel
debug
remotecontrol
similarstructures
shape
device
linux
rna
modelcif
measure
alphafold
define
esmfold
registration
mutationscores
modeller
ui
matchmaker
mmaker

Same snippet yields no output in a newly-opened session.

comment:2 by Eric Pettersen, 9 months ago

Cc: Tony Schaefer added
Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Status: new → assigned
Summary: ChimeraX bug report submission → Installing SEQCROW nukes multiple unrelated commands

comment:3 by Tony Schaefer, 9 months ago 

I'm not sure this is specific to seqcrow, but it is interesting that you're
not getting any output for that snippet sometimes. My list doesn't have
linux, matchmaker, or mmaker on it though. I've tried running this on
Windows, and I always get output from it. Many of these appear to be
commands that only have subcommands. I don't think many of these actually
have their own description (their subcommands do). Are these commands
registered in the fresh session?

On Wed, Jan 15, 2025 at 12:41 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>

comment:4 by Tristan Croll, 9 months ago

Ok, definitely not something specific to seqcrow - I get exactly the same behaviour (on my Windows machine - initial report was in Linux) in a session after installing the QScore plugin. Think it's most likely something to do with the toolshed install code. Somewhat minor given it only seems to affect the session which was used to actually install the bundle.

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