id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14723	Problem with MSF alignment file	sanjana.vasanth@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Unable to open .msf file in sequence viewer

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show ""Show Sequence Viewer""

> show # target m

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> open ""D:/Thesis/Data/Skanda/Sequence alignment/Sequences -
> Copy/muscle_aligned.msf""

Summary of feedback from opening D:/Thesis/Data/Skanda/Sequence
alignment/Sequences - Copy/muscle_aligned.msf  
---  
notes | Alignment identifier is muscle_aligned.msf  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> select

Nothing selected  

> ui tool show ""Show Sequence Viewer""

> open ""D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf"" format msf

Summary of feedback from opening D:\Thesis\Data\Skanda\Sequence
alignment\Sequences - Copy\muscle_aligned.msf  
---  
notes | Alignment identifier is muscle_aligned.msf  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> open ""D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf"" format msf

Summary of feedback from opening D:\Thesis\Data\Skanda\Sequence
alignment\Sequences - Copy\muscle_aligned.msf  
---  
notes | Destroying pre-existing alignment with identifier muscle_aligned.msf  
Alignment identifier is muscle_aligned.msf  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> ~hbonds

> hbonds reveal true

Atom specifier selects no atoms  

> interfaces ~solvent

No atoms specified  

> color bynucleotide

> color bfactor

No atoms specified  

> open ""D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf"" format msf

Summary of feedback from opening D:\Thesis\Data\Skanda\Sequence
alignment\Sequences - Copy\muscle_aligned.msf  
---  
notes | Destroying pre-existing alignment with identifier muscle_aligned.msf  
Alignment identifier is muscle_aligned.msf  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> close #

Expected a models specifier or a keyword  

> ui windowfill toggle

[Repeated 1 time(s)]

> ui tool show ""Blast Protein""

> open ""D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf"" format msf

Summary of feedback from opening D:\Thesis\Data\Skanda\Sequence
alignment\Sequences - Copy\muscle_aligned.msf  
---  
notes | Destroying pre-existing alignment with identifier muscle_aligned.msf  
Alignment identifier is muscle_aligned.msf  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> open ""D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf"" format msf

Summary of feedback from opening D:\Thesis\Data\Skanda\Sequence
alignment\Sequences - Copy\muscle_aligned.msf  
---  
notes | Destroying pre-existing alignment with identifier muscle_aligned.msf  
Alignment identifier is muscle_aligned.msf  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> open ""D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf"" format fasta

No sequences found in FASTA file 'muscle_aligned.msf'!  

> open ""D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf"" format afas

Invalid ""format"" argument: Should be one of 'aln', 'amber', 'amira', 'apbs',
'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'clustal', 'cmap', 'cmd', 'cod',
'collada', 'compiled python', 'corecif', 'cube', 'dcd', 'defattr', 'delphi',
'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol',
'gro', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imod', 'imodmap',
'ims', 'iupac', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mole',
'mrc', 'msf', 'netcdfmap', 'nifti', 'nrrd', 'obj', 'pcod', 'pdb', 'pdbqt',
'pfam', 'photo', 'pif', 'pir', 'positions', 'priism', 'profec', 'pseudobonds',
'psf', 'python', 'rsf', 'schrodinger maestro', 'sdf', 'segger', 'session',
'sff', 'situs', 'smallcif', 'smiles', 'spider', 'stl', 'stockholm', 'storm',
'swc', 'swissdock', 'tom_em', 'trr', 'uhbd', 'uniprot', 'viperdb', 'vtk', 'web
fetch', 'xplor', 'xtc', or 'zdock'  

> open ""D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf"" format aln

Cannot open files: Syntax error in ALN file 'muscle_aligned.msf': First non-
blank line does not start with 'CLUSTAL'  

> open ""D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf"" format msn

Invalid ""format"" argument: Should be one of 'aln', 'amber', 'amira', 'apbs',
'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'clustal', 'cmap', 'cmd', 'cod',
'collada', 'compiled python', 'corecif', 'cube', 'dcd', 'defattr', 'delphi',
'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol',
'gro', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imod', 'imodmap',
'ims', 'iupac', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mole',
'mrc', 'msf', 'netcdfmap', 'nifti', 'nrrd', 'obj', 'pcod', 'pdb', 'pdbqt',
'pfam', 'photo', 'pif', 'pir', 'positions', 'priism', 'profec', 'pseudobonds',
'psf', 'python', 'rsf', 'schrodinger maestro', 'sdf', 'segger', 'session',
'sff', 'situs', 'smallcif', 'smiles', 'spider', 'stl', 'stockholm', 'storm',
'swc', 'swissdock', 'tom_em', 'trr', 'uhbd', 'uniprot', 'viperdb', 'vtk', 'web
fetch', 'xplor', 'xtc', or 'zdock'  




OpenGL version: 3.3.0 NVIDIA 546.26
OpenGL renderer: NVIDIA GeForce MX130/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP Pavilion Laptop 15-cs1xxx
OS: Microsoft Windows 10 Home Single Language (Build 19045)
Memory: 8,471,760,896
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    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: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

}}}
"	defect	feedback	normal		Sequence								all	ChimeraX