MD Viewer: opening non-trajectory

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.8.0-55-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/gbolcato/Desktop/symeres/allegati/traj.pdb

Chain information for traj.pdb  
---  
Chain | Description  
1.1/X 1.2/X 1.3/X 1.4/X 1.5/X 1.6/X 1.7/X 1.8/X 1.9/X 1.10/X 1.11/X 1.12/X
1.13/X 1.14/X 1.15/X 1.16/X 1.17/X 1.18/X 1.19/X 1.20/X 1.21/X 1.22/X 1.23/X
1.24/X 1.25/X 1.26/X 1.27/X 1.28/X 1.29/X 1.30/X 1.31/X 1.32/X 1.33/X 1.34/X
1.35/X 1.36/X 1.37/X 1.38/X 1.39/X 1.40/X 1.41/X 1.42/X 1.43/X 1.44/X 1.45/X
1.46/X 1.47/X 1.48/X 1.49/X 1.50/X 1.51/X 1.52/X 1.53/X 1.54/X 1.55/X 1.56/X
1.57/X 1.58/X 1.59/X 1.60/X 1.61/X 1.62/X 1.63/X 1.64/X 1.65/X 1.66/X 1.67/X
1.68/X 1.69/X 1.70/X 1.71/X 1.72/X 1.73/X 1.74/X 1.75/X 1.76/X 1.77/X 1.78/X
1.79/X 1.80/X 1.81/X 1.82/X 1.83/X 1.84/X 1.85/X 1.86/X 1.87/X 1.88/X 1.89/X
1.90/X 1.91/X 1.92/X 1.93/X 1.94/X 1.95/X 1.96/X 1.97/X 1.98/X 1.99/X 1.100/X
1.101/X 1.102/X 1.103/X 1.104/X 1.105/X 1.106/X 1.107/X 1.108/X 1.109/X
1.110/X 1.111/X 1.112/X 1.113/X 1.114/X 1.115/X 1.116/X | No description
available  
  

> close session

> open /home/gbolcato/Desktop/symeres/allegati/rec.top

Unrecognized file suffix '.top'  

> open /home/gbolcato/Desktop/symeres/allegati/rec.prmtop

Unrecognized file suffix '.prmtop'  

> open /home/gbolcato/Desktop/symeres/allegati/dry_1.pdb

Summary of feedback from opening
/home/gbolcato/Desktop/symeres/allegati/dry_1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Selection 'protein or resn... or resname CYM'  
  
Chain information for dry_1.pdb #1  
---  
Chain | Description  
| No description available  
  

> ui tool show "Molecular Dynamics Viewer"

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

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 629, in customEvent  
func(*args, **kw)  
File "/home/gbolcato/.local/share/ChimeraX/1.1/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme  
self.openFile()  
File "/home/gbolcato/.local/share/ChimeraX/1.1/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/home/gbolcato/.local/share/ChimeraX/1.1/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 20.2.6
OpenGL renderer: Mesa Intel(R) UHD Graphics 620 (WHL GT2)
OpenGL vendor: Intel
Manufacturer: Micro-Star International Co., Ltd.
Model: PS63 Modern 8RC
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi       2.6Gi        26Gi       563Mi       2.5Gi        27Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 (Whiskey Lake) [8086:3ea0]	
	DeviceName: Onboard - Video	
	Subsystem: Micro-Star International Co., Ltd. [MSI] UHD Graphics 620 (Whiskey Lake) [1462:126c]
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    MolecularDynamicsViewer: 1.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2