Opened 13 months ago

Last modified 13 months ago

#16080 assigned defect

SEQCROW: substitute: residue names must be 4 characters or less

Reported by: chimerax-bug-report@… Owned by: Tony Schaefer
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "2D Builder"

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

getting structure  

> ui mousemode right substitute

> substitute /a:1@H11 substituents iPr minimize true newName eq-ipr-
> sikloheksana newResidue false useRemoteness false

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 656, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 556, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Users\Fanny Raniah N\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\mouse_modes.py", line 991, in mouse_up  
run(  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Fanny Raniah N\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\commands\substitute.py", line 124, in substitute  
raise RuntimeError("residue names must be 4 characters or less")  
RuntimeError: residue names must be 4 characters or less  

RuntimeError: residue names must be 4 characters or less  

File "C:\Users\Fanny Raniah N\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\commands\substitute.py", line 124, in substitute  
raise RuntimeError("residue names must be 4 characters or less")  

See log for complete Python traceback.  





OpenGL version: 3.3.0 - Build 27.20.100.9565
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: HUAWEI
Model: KLVD-WXX9
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 8,379,490,304
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: en-US

Installed Packages:
   alabaster: 0.7.16
   appdirs: 1.4.4
   asttokens: 2.4.1
   Babel: 2.15.0
   beautifulsoup4: 4.12.3
   blockdiag: 3.0.0
   blosc2: 2.0.0
   build: 1.2.1
   certifi: 2024.6.2
   cftime: 1.6.4
   charset-normalizer: 3.3.2
   ChimeraX-AddCharge: 1.5.17
   ChimeraX-AddH: 2.2.6
   ChimeraX-AlignmentAlgorithms: 2.0.2
   ChimeraX-AlignmentHdrs: 3.5
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.12.7
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.1.1
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.57.1
   ChimeraX-AtomicLibrary: 14.0.6
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.4
   ChimeraX-BasicActions: 1.1.2
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 2.4.6
   ChimeraX-BondRot: 2.0.4
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.12.1
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.2.7
   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: 2.2.4
   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: 1.8
   ChimeraX-CoreFormats: 1.2
   ChimeraX-coulombic: 1.4.3
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.3
   ChimeraX-Dicom: 1.2.4
   ChimeraX-DiffPlot: 1.0
   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: 1.1.1
   ChimeraX-Hbonds: 2.4
   ChimeraX-Help: 1.2.2
   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-IUPAC: 1.0
   ChimeraX-Label: 1.1.10
   ChimeraX-ListInfo: 1.2.2
   ChimeraX-Log: 1.1.6
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.9.1
   ChimeraX-Map: 1.2
   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: 2.1.3
   ChimeraX-MCopy: 1.0
   ChimeraX-MDcrds: 2.7.1
   ChimeraX-MedicalToolbar: 1.0.3
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.14.1
   ChimeraX-MMTF: 2.2
   ChimeraX-Modeller: 1.5.17
   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-Neuron: 1.0
   ChimeraX-Nifti: 1.2
   ChimeraX-NMRSTAR: 1.0.2
   ChimeraX-NRRD: 1.2
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.13.5
   ChimeraX-PDB: 2.7.5
   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: 1.1.1
   ChimeraX-PubChem: 2.2
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.2
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.4.1
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.2
   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: 3.0.15
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.11.2
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.1.1
   ChimeraX-ShowSequences: 1.0.3
   ChimeraX-SideView: 1.0.1
   ChimeraX-Smiles: 2.1.2
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.16.5
   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: 1.1.2
   ChimeraX-ToolshedUtils: 1.2.4
   ChimeraX-Topography: 1.0
   ChimeraX-ToQuest: 1.0
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.39.1
   ChimeraX-uniprot: 2.3
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.4.3
   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
   comtypes: 1.4.1
   contourpy: 1.2.1
   cxservices: 1.2.2
   cycler: 0.12.1
   Cython: 3.0.10
   debugpy: 1.8.1
   decorator: 5.1.1
   docutils: 0.20.1
   executing: 2.0.1
   filelock: 3.13.4
   fonttools: 4.53.0
   funcparserlib: 2.0.0a0
   glfw: 2.7.0
   grako: 3.16.5
   h5py: 3.11.0
   html2text: 2024.2.26
   idna: 3.7
   ihm: 1.0
   imagecodecs: 2024.1.1
   imagesize: 1.4.1
   ipykernel: 6.29.2
   ipython: 8.21.0
   ipywidgets: 8.1.3
   jedi: 0.19.1
   jinja2: 3.1.4
   jupyter-client: 8.6.0
   jupyter-core: 5.7.2
   jupyterlab-widgets: 3.0.11
   kiwisolver: 1.4.5
   line-profiler: 4.1.2
   lxml: 5.2.1
   lz4: 4.3.3
   MarkupSafe: 2.1.5
   matplotlib: 3.8.4
   matplotlib-inline: 0.1.7
   msgpack: 1.0.8
   nest-asyncio: 1.6.0
   netCDF4: 1.6.5
   networkx: 3.3
   nibabel: 5.2.0
   nptyping: 2.5.0
   numexpr: 2.10.0
   numpy: 1.26.4
   openvr: 1.26.701
   packaging: 24.1
   ParmEd: 4.2.2
   parso: 0.8.4
   pep517: 0.13.1
   pillow: 10.3.0
   pip: 24.0
   pkginfo: 1.10.0
   platformdirs: 4.2.2
   prompt-toolkit: 3.0.47
   psutil: 5.9.8
   pure-eval: 0.2.2
   py-cpuinfo: 9.0.0
   pycollada: 0.8
   pydicom: 2.4.4
   pygments: 2.17.2
   pynmrstar: 3.3.4
   pynrrd: 1.0.0
   PyOpenGL: 3.1.7
   PyOpenGL-accelerate: 3.1.7
   pyopenxr: 1.0.3401
   pyparsing: 3.1.2
   pyproject-hooks: 1.1.0
   PyQt6-commercial: 6.6.1
   PyQt6-Qt6: 6.6.3
   PyQt6-sip: 13.6.0
   PyQt6-WebEngine-commercial: 6.6.0
   PyQt6-WebEngine-Qt6: 6.6.3
   python-dateutil: 2.9.0.post0
   pytz: 2024.1
   pywin32: 306
   pyzmq: 26.0.3
   qtconsole: 5.5.1
   QtPy: 2.4.1
   RandomWords: 0.4.0
   requests: 2.31.0
   scipy: 1.13.0
   Send2Trash: 1.8.3
   SEQCROW: 1.8.12
   setuptools: 69.5.1
   sfftk-rw: 0.8.1
   six: 1.16.0
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   soupsieve: 2.5
   sphinx: 7.2.6
   sphinx-autodoc-typehints: 2.0.1
   sphinxcontrib-applehelp: 1.0.8
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 1.0.6
   sphinxcontrib-htmlhelp: 2.0.5
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 1.0.7
   sphinxcontrib-serializinghtml: 1.1.10
   stack-data: 0.6.3
   superqt: 0.6.3
   tables: 3.8.0
   tcia-utils: 1.5.1
   tifffile: 2024.1.30
   tinyarray: 1.2.4
   tornado: 6.4.1
   traitlets: 5.14.2
   typing-extensions: 4.12.2
   tzdata: 2024.1
   urllib3: 2.2.1
   wcwidth: 0.2.13
   webcolors: 1.13
   wheel: 0.43.0
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.11
   WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 13 months ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SEQCROW: substitute: residue names must be 4 characters or less

You might want to raise chimerax.core.errors.UserError (or .LimitationError) here so that the user sees the message but it doesn't produce a traceback and bug report.

Last edited 13 months ago by Eric Pettersen (previous) (diff)

comment:2 by Tony Schaefer, 13 months ago 

Thanks, I've turned this into a LimitationError

On Mon, Oct 7, 2024 at 3:21 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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