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Opened 10 months ago
Last modified 10 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 , 10 months ago
| Platform: | → all |
|---|---|
| Project: | → ChimeraX |
comment:2 by , 10 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Installing SEQCROW nukes multiple unrelated commands |
comment:3 by , 10 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 , 10 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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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 mmakerSame snippet yields no output in a newly-opened session.