Opened 3 months ago

Closed 3 months ago

#18464 closed defect (duplicate)

Regular PDB file opened in MD Viewer

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
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:        Linux-6.8.0-71-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/ranjan/gromacs simulations/Mettl14 complex/complex.gro" format
> gro

Chain information for Glycine aRginine prOline Methionine Alanine Cystine
Serine #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open "/home/ranjan/gromacs simulations/Mettl14 complex/fit.xtc"

Replaced existing frames of Glycine aRginine prOline Methionine Alanine
Cystine Serine #1 with 1001 new frames  

> view

> select ::name="NIY"

23 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel atoms

> label :NIY size 3 color black

> label :NIY

> graphics text method solid

Expected a keyword  

> graphics antialiasing true

Expected a keyword  

> graphics text pixels false

Expected a keyword  

> select add #1.1

23 atoms, 23 bonds, 1 residue, 2 models selected  

> select subtract #1.1

23 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #1.1

23 atoms, 23 bonds, 1 residue, 2 models selected  

> select subtract #1.1

23 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #1.1

23 atoms, 23 bonds, 1 residue, 2 models selected  

> select subtract #1.1

23 atoms, 23 bonds, 1 residue, 1 model selected  

> label :NIY size 4 color black bgColor none style bold

Expected a keyword  

> label :NIY size 10

> label :NIY size 30

> label :NIY size 50

[Repeated 1 time(s)]

> label :NIY size 20 color black bgColor none style bold

Expected a keyword  

> label font "Arial Bold"

[Repeated 1 time(s)]

> label :NIY size 80

> label font "Arial Bold"

> select clear

[Repeated 1 time(s)]

> ui mousemode right "resize markers"

[Repeated 1 time(s)]

> select clear

[Repeated 1 time(s)]

> ui mousemode right label

> select /B:198@CG

1 atom, 1 residue, 1 model selected  

> select /B:198

23 atoms, 23 bonds, 1 residue, 1 model selected  

> select /B:208

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /B:208

15 atoms, 14 bonds, 1 residue, 1 model selected  

> ui mousemode right label

[Repeated 1 time(s)]

> label #1/B:198

[Repeated 1 time(s)]

> label #1/B:208

> label :NIY size 500

> label :NIY size 2000

Label width 9473 exceeds maximum 4096 and will be clipped  

> label :NIY size 500

> select ::name="NIY"

23 atoms, 23 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

1243 hydrogen bonds found in 1001 coordsets  

> style hbonds width 4

Expected a keyword  

> models

Unknown command: models  

>

Incomplete command: modelcif  

> setattr p width 4 :@hbonds

Expected a keyword  

> setattr p width 4 :@hbonds

Expected a keyword  

> setattr p width 4 #1.2

Expected a keyword  

> setattr p pseudobond width 4 #1.2

Expected a keyword  

> setattr p width 6 #1.2

Expected a keyword  

> setattr p width #1.2 6

Expected a keyword  

> setattr p width #1.2 4

Expected a keyword  

> setattr #1.2 p width 4

Assigning width attribute to 1 item  
Not creating attribute 'width'; use 'create true' to override  

> setattr #1.2 p width 4 create true

Assigning width attribute to 1 item  

> setattr #1.2 p width 20 create true

Assigning width attribute to 1 item  

> select clear

> setattr #1.2 p width 4 create true

Assigning width attribute to 1 item  

> label #1/B:198

> ui mousemode right label

> ui mousemode right "move label"

> ui mousemode right "color key"

> key delete

> select /B:195

19 atoms, 18 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /B:198

23 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel atoms

> ui mousemode right label

[Repeated 1 time(s)]

> label #1/B:195

> ui mousemode right "move label"

> view clip false

[Repeated 1 time(s)]

> show target m

[Repeated 1 time(s)]

> view clip false

> ui windowfill toggle

[Repeated 1 time(s)]

> open "/home/ranjan/gromacs simulations/Mettl14 complex/fit.xtc"

Replaced existing frames of Glycine aRginine prOline Methionine Alanine
Cystine Serine #1 with 1001 new frames  

> ui tool show "Molecular Dynamics Viewer"

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 316, in interceptRequest  
self._callback(info)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 479, in thread_safe  
func(*args, **kw)  
File "/home/ranjan/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme  
self.openFile()  
File "/home/ranjan/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 239, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
~~~~~~~~~~~~~~~~~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/home/ranjan/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 239, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
~~~~~~~~~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 316, in interceptRequest  
self._callback(info)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 479, in thread_safe  
func(*args, **kw)  
File "/home/ranjan/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme  
self.openFile()  
File "/home/ranjan/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 239, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
~~~~~~~~~~~~~~~~~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/home/ranjan/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 239, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
~~~~~~~~~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 550.163.01
OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_IN.ISO8859-1
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7E06
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 28 Intel(R) Core(TM) i7-14700K
Cache Size: 33792 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       6.0Gi       5.8Gi       208Mi       4.1Gi       9.4Gi
	Swap:           15Gi       256Ki        15Gi

Graphics:
	04:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA106 [GeForce RTX 3060 Lite Hash Rate] [10de:2504] (rev a1)	
	Subsystem: NVIDIA Corporation GA106 [GeForce RTX 3060 Lite Hash Rate] [10de:1536]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2025.6.15
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by Eric Pettersen, 3 months ago

Component: Unassigned → Third Party
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Regular PDB file opened in MD Viewer

comment:2 by Eric Pettersen, 3 months ago

Resolution: → duplicate
Status: accepted → closed
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