Opened 13 months ago

Closed 13 months ago

Last modified 13 months ago

#16128 closed defect (limitation)

MolecularDynamicsViewer: list index out of range

Reported by: sebastien.gounel@… 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:        Windows-10-10.0.19045
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
I try to open a multiframe PDB file to visualize a MD on chimeraX

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 "Molecular Dynamics Viewer"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py",
line 423, in thread_safe  
func(*args, **kw)  
File "D:\Users\gounel\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "D:\Users\gounel\AppData\Local\UCSF\ChimeraX\1.8\Python311\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 "D:\Users\gounel\AppData\Local\UCSF\ChimeraX\1.8\Python311\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 "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py",
line 423, in thread_safe  
func(*args, **kw)  
File "D:\Users\gounel\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "D:\Users\gounel\AppData\Local\UCSF\ChimeraX\1.8\Python311\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 "D:\Users\gounel\AppData\Local\UCSF\ChimeraX\1.8\Python311\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 552.74
OpenGL renderer: NVIDIA GeForce RTX 3080 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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

Manufacturer: Dell Inc.
Model: Precision 7760
OS: Microsoft Windows 10 Professionnel (Build 19045)
Memory: 33,581,043,712
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11850H @ 2.50GHz
OSLanguage: fr-FR

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
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    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
    MolecularDynamicsViewer: 1.6
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Change History (7)

comment:1 by Eric Pettersen, 13 months ago

Component: Unassigned → Third Party
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → MolecularDynamicsViewer: list index out of range

comment:2 by Eric Pettersen, 13 months ago

Resolution: → limitation
Status: accepted → closed

Hi Sebastien,

This error indicated that your PDB isn't a correct multi-MODEL PDB file -- it lacks MODEL/ENDMDL records denoting the frames.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by sebastien.gounel@…, 13 months ago 

Hello,

Thank you for your response.

Currently, I have a set of PDB files that correspond to a molecular dynamics simulation, which I have combined into one using the "cat" command in Linux. When I use this file in VMD, it works perfectly.

Could you please guide me on the correct procedure to follow so that it works correctly in XChimera?

Best regards
Sébastien

----- Mail original -----
De: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
À: pett@cgl.ucsf.edu, "sebastien gounel" <sebastien.gounel@crpp.cnrs.fr>
Envoyé: Lundi 14 Octobre 2024 07:33:24
Objet: Re: [ChimeraX] #16128: MolecularDynamicsViewer: list index out of range

#16128: MolecularDynamicsViewer: list index out of range
-----------------------------------------+--------------------
          Reporter:  sebastien.gounel@\u2026  |      Owner:  pett
              Type:  defect              |     Status:  closed
          Priority:  normal              |  Milestone:
         Component:  Third Party         |    Version:
        Resolution:  limitation          |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+--------------------
Changes (by pett):

 * resolution:   => limitation
 * status:  accepted => closed

Comment:

 Hi Sebastien,
         This error indicated that your PDB isn't a correct multi-MODEL PDB
 file -- it lacks MODEL/ENDMDL records denoting the frames.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

comment:4 by Eric Pettersen, 13 months ago

I don't think there is a way to read them into ChimeraX as a trajectory without tediously prepending/appending MODEL/ENDMDL records to each file and then catting them all together. Don't you have the trajectory output in some more concise format than PDB files? ChimeraX can read Amber NetCDF, Charmm/NAMD DCD, Gromacs XTC and TRR format coordinate files, as per ​https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory

--Eric

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

comment:5 by Eric Pettersen, 13 months ago

P.S. Our servers were down for maintenance all week, so this has been my first opportunity to respond.

comment:6 by sebastien.gounel@…, 13 months ago 

OK I going to try. I just test this pdb file because I download this addon where is precise to read pdb stack.
Thanks for the linck I'm going to make some tests

best regards

----- Mail original -----
De: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
À: "sebastien gounel" <sebastien.gounel@crpp.cnrs.fr>, "pett" <pett@cgl.ucsf.edu>
Envoyé: Samedi 19 Octobre 2024 02:33:30
Objet: Re: [ChimeraX] #16128: MolecularDynamicsViewer: list index out of range

#16128: MolecularDynamicsViewer: list index out of range
-----------------------------------------+--------------------
          Reporter:  sebastien.gounel@\u2026  |      Owner:  pett
              Type:  defect              |     Status:  closed
          Priority:  normal              |  Milestone:
         Component:  Third Party         |    Version:
        Resolution:  limitation          |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+--------------------
Comment (by pett):

 I don't there is a way to read them into ChimeraX as a trajectory without
 tediously prepending/appending MODEL/ENDMDL records to each file and then
 catting them all together.  Don't you have the trajectory output in some
 more concise format than PDB files?  ChimeraX can read Amber NetCDF,
 Charmm/NAMD DCD, Gromacs XTC and TRR format coordinate files, as per
 https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory

 --Eric

comment:7 by Eric Pettersen, 13 months ago

I hope it works. Let me know if you run into trouble.

--Eric

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