Molecular Dynamics Viewer: list index out of range

[pamela.beaurregard@…]

The following bug report has been submitted:
Platform:        macOS-11.7.10-x86_64-i386-64bit
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  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> ui tool show "Molecular Dynamics Viewer"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe  
func(*args, **kw)  
File "/Users/Permafrost/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme  
self.openFile()  
File "/Users/Permafrost/Library/Application
Support/ChimeraX/1.8/lib/python/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 "/Users/Permafrost/Library/Application
Support/ChimeraX/1.8/lib/python/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.  
  

> toolshed show

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe  
func(*args, **kw)  
File "/Users/Permafrost/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme  
self.openFile()  
File "/Users/Permafrost/Library/Application
Support/ChimeraX/1.8/lib/python/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 "/Users/Permafrost/Library/Application
Support/ChimeraX/1.8/lib/python/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: 4.1 INTEL-16.5.14
OpenGL renderer: Intel Iris OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 478.0.0.0.0
      SMC Version (system): 2.16f68

Software:

    System Software Overview:

      System Version: macOS 11.7.10 (20G1427)
      Kernel Version: Darwin 20.6.0
      Time since boot: 10 days 23:14

Graphics/Displays:

    Intel Iris:

      Chipset Model: Intel Iris
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0a2e
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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    appdirs: 1.4.4
    appnope: 0.1.4
    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: 2023.11.17
    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
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    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
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    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
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    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
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    colorama: 0.4.6
    comm: 0.2.2
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    cycler: 0.12.1
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    executing: 2.0.1
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    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
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    ipykernel: 6.29.2
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    ipywidgets: 8.1.3
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    PyQt6-WebEngine-commercial: 6.6.0
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    python-dateutil: 2.9.0.post0
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[Eric Pettersen]

Hi Pamela,

The Molecular Dynamics Viewer is for showing a multi-MODEL PDB file as a trajectory. If you open a normal single-structure one-MODEL PDB file with it, you get the error you saw. You can open such files directly in ChimeraX with its "open" command or File→Open menu item.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[pamela.beaurregard@…]

Hey eric,

I did what you said i opened the file and try to run the molecular dynamics but the error persist. I just need your help to know what i need to put on the  Out put trajectory file and the output restar trajectory file.  cause is very confuse and it wont let me get the molecular dynamics result.

thank you so much

AttributeError: '_molecule.Atom' object has no attribute 'gaffType'

  File "/Applications/Chimera.app/Contents/Resources/share/MMMD/MMTKinter.py", line 695, in _addStandardResidue
    "amber_atom_type": a.gaffType,

See reply log for Python traceback.
________________________________
De: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Enviado: lunes, 7 de abril de 2025 3:23 p. m.
Para: Pamela Iztniel Beaurregard Eloy <pamela.beaurregard@cinvestav.mx>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Asunto: Re: [ChimeraX] #17314: Molecular Dynamics Viewer: list index out of range

Precaución: Este correo se originó desde fuera de la Institución. No haga clic en enlaces ni abra archivos adjuntos, a menos que reconozca al remitente y tenga conocimiento de que el contenido es seguro.


#17314: Molecular Dynamics Viewer: list index out of range
-------------------------------------------+--------------------
          Reporter:  pamela.beaurregard@…  |      Owner:  pett
              Type:  defect                |     Status:  closed
          Priority:  normal                |  Milestone:
         Component:  MD/Ensemble Analysis  |    Version:
        Resolution:  not a bug             |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+--------------------
Changes (by pett):

 * resolution:   => not a bug
 * status:  accepted => closed

Comment:

 Hi Pamela,
         The Molecular Dynamics Viewer is for showing a multi-MODEL PDB
 file as a trajectory.  If you open a normal single-structure one-MODEL PDB
 file with it, you get the error you saw.  You can open such files directly
 in ChimeraX with its "open" command or File→Open menu item.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17314#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker


________________________________

De conformidad con el inciso a) del Artículo 57 del "Acuerdo por el que se emiten las políticas y disposiciones para impulsar el uso y aprovechamiento de la informática, el gobierno digital, las tecnologías de la información y comunicación, y la seguridad de la información en la Administración Pública Federal" publicado en el Diario Oficial de la Federación el 6 de septiembre del 2021. La información contenida en correos institucionales es de carácter confidencial y su tratamiento es con estricta observancia a los principios de licitud, finalidad, lealtad, consentimiento, calidad, proporcionalidad, información y responsabilidad establecidos en la Ley General de Protección de Datos Personales de Sujetos Obligados.


________________________________

De conformidad con el inciso a) del Artículo 57 del "Acuerdo por el que se emiten las políticas y disposiciones para impulsar el uso y aprovechamiento de la informática, el gobierno digital, las tecnologías de la información y comunicación, y la seguridad de la información en la Administración Pública Federal" publicado en el Diario Oficial de la Federación el 6 de septiembre del 2021. La información contenida en correos institucionales es de carácter confidencial y su tratamiento es con estricta observancia a los principios de licitud, finalidad, lealtad, consentimiento, calidad, proporcionalidad, información y responsabilidad establecidos en la Ley General de Protección de Datos Personales de Sujetos Obligados.

[Eric Pettersen]

Hi Pamela,

The first error you reported was for viewing a trajectory in ChimeraX. The error you're reporting now is for generating a trajectory in Chimera. Those are two different things and two different programs. In order to help you with the second error I need you to get the error again and then use the "Report Bug" button on the error dialog to submit a full bug report to the Chimera bug-tracking system.

--Eric

[pamela.beaurregard@…]

Hello Eric,

I hope your having a good day. Eric about the last message you told me that
The Molecular Dynamics Viewer is for showing a multi-MODEL PDB
 file as a trajectory. If you open a normal single-structure one-MODEL PDB
  file with it, you get the error you saw.  You can open such files
 directly in ChimeraX with its "open" command or File→Open menu item.

 I need to molecular dynamics of an especific molecule; but i just have one pbd file, i dont get what other files i need to open. Can you explain me more.

thank you so much.
Pam


________________________________
De: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Enviado: jueves, 10 de abril de 2025 2:20 p. m.
Para: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Pamela Iztniel Beaurregard Eloy <pamela.beaurregard@cinvestav.mx>
Asunto: Re: [ChimeraX] #17314: Molecular Dynamics Viewer: list index out of range

Precaución: Este correo se originó desde fuera de la Institución. No haga clic en enlaces ni abra archivos adjuntos, a menos que reconozca al remitente y tenga conocimiento de que el contenido es seguro.


#17314: Molecular Dynamics Viewer: list index out of range
-------------------------------------------+--------------------
          Reporter:  pamela.beaurregard@…  |      Owner:  pett
              Type:  defect                |     Status:  closed
          Priority:  normal                |  Milestone:
         Component:  MD/Ensemble Analysis  |    Version:
        Resolution:  not a bug             |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+--------------------
Comment (by pett):

 Hi Pamela,
         The first error you reported was for viewing a trajectory in
 ChimeraX.  The error you're reporting now is for generating a trajectory
 in Chimera.  Those are two different things and two different programs.
 In order to help you with the second error I need you to get the error
 again and then use the "Report Bug" button on the error dialog to submit a
 full bug report to the Chimera bug-tracking system.

 --Eric
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17314#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker


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De conformidad con el inciso a) del Artículo 57 del "Acuerdo por el que se emiten las políticas y disposiciones para impulsar el uso y aprovechamiento de la informática, el gobierno digital, las tecnologías de la información y comunicación, y la seguridad de la información en la Administración Pública Federal" publicado en el Diario Oficial de la Federación el 6 de septiembre del 2021. La información contenida en correos institucionales es de carácter confidencial y su tratamiento es con estricta observancia a los principios de licitud, finalidad, lealtad, consentimiento, calidad, proporcionalidad, información y responsabilidad establecidos en la Ley General de Protección de Datos Personales de Sujetos Obligados.


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De conformidad con el inciso a) del Artículo 57 del "Acuerdo por el que se emiten las políticas y disposiciones para impulsar el uso y aprovechamiento de la informática, el gobierno digital, las tecnologías de la información y comunicación, y la seguridad de la información en la Administración Pública Federal" publicado en el Diario Oficial de la Federación el 6 de septiembre del 2021. La información contenida en correos institucionales es de carácter confidencial y su tratamiento es con estricta observancia a los principios de licitud, finalidad, lealtad, consentimiento, calidad, proporcionalidad, información y responsabilidad establecidos en la Ley General de Protección de Datos Personales de Sujetos Obligados.

[Eric Pettersen]

In Chimera (not ChimeraX), open your PDB file. Since some of the hydrogens in the PDB have non-standard names, delete all hydrogens by opening the command line (Favorites→Command Line) and typing "del H" and then hitting Return. Then use the Tools→MD/Ensemble Analysis→Molecular Dynamics Simulation tool to launch your MD simulation. That tool isn't simple to use, but it is thoroughly explained if you click its Help button.