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#16388 closed defect (not a bug)

Viewing Gromacs output

Reported by:	jhmvangils@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	MD/Ensemble Analysis	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
I want to view an MD simulation from Gromacs. In the old version of Chimera this was easy, using the xtc and trr files. In the new version, the tool is no longer available. I installed Molecular Dynamics Viewer, but that gives an error when I load in a PDB file. Could you fix the bug, or let me know what the best way is to view MD trajectories in ChimeraX? Thanks

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 "C:\Users\kpzj160\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "C:\Users\kpzj160\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 "C:\Users\kpzj160\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 "C:\Users\kpzj160\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "C:\Users\kpzj160\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 "C:\Users\kpzj160\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 "C:\Users\kpzj160\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "C:\Users\kpzj160\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 "C:\Users\kpzj160\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.  
  

> toolshed show

> open "C:/Users/kpzj160/OneDrive - Neogene Therapeutics,
> Inc/Documents/Downloads_old/all_structures/raw/1ao7.pdb"

1ao7.pdb title:  
Complex between human T-cell receptor, viral peptide (tax), and hla-A 0201
[more info...]  
  
Chain information for 1ao7.pdb #2  
---  
Chain | Description | UniProt  
A | HLA-A2 heavy chain | 1A02_HUMAN 1-275  
B | β-2 microglobulin | B2MG_HUMAN 1-99  
C | tax peptide | TAT_HTL1C 1-9  
D | T cell receptor α |   
E | T cell receptor β |   
  
Non-standard residues in 1ao7.pdb #2  
---  
EMC — ethyl mercury ion  
  

> hide atoms

> show cartoons

> hide #!2 models

> hide #1 models

> select subtract #1

Nothing selected  

> show #!2 models

> select add #2

5711 atoms, 5832 bonds, 5 pseudobonds, 746 residues, 3 models selected  

> select subtract #1

5711 atoms, 5832 bonds, 5 pseudobonds, 746 residues, 3 models selected  
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 "C:\Users\kpzj160\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "C:\Users\kpzj160\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 "C:\Users\kpzj160\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.  
  

> close session

> open "C:\Users\kpzj160\OneDrive - Neogene Therapeutics,
> Inc\Documents\Downloads_old\all_structures\raw\1ao7.pdb" coorsets=True

'coorsets=True' has no suffix  

> open "C:\Users\kpzj160\OneDrive - Neogene Therapeutics,
> Inc\Documents\Downloads_old\all_structures\raw\1ao7.pdb" coorsets True

'coorsets' has no suffix  

> open "C:\Users\kpzj160\OneDrive - Neogene Therapeutics,
> Inc\Documents\Downloads_old\all_structures\raw\1ao7.pdb" coordsets true

1ao7.pdb title:  
Complex between human T-cell receptor, viral peptide (tax), and hla-A 0201
[more info...]  
  
Chain information for 1ao7.pdb #1  
---  
Chain | Description | UniProt  
A | HLA-A2 heavy chain | 1A02_HUMAN 1-275  
B | β-2 microglobulin | B2MG_HUMAN 1-99  
C | tax peptide | TAT_HTL1C 1-9  
D | T cell receptor α |   
E | T cell receptor β |   
  
Non-standard residues in 1ao7.pdb #1  
---  
EMC — ethyl mercury ion  
  
1ao7.pdb has 1 coordinate sets  

> open C:\Users\kpzj160\Downloads\md_20ns_1ao7_full.xtc structureModel #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\md_crds\\__init__.py", line 115, in open  
num_coords = read_coords(session, data, structure_model, md_type,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 33, in read_coords  
coords = array(coords_list, dtype=float64)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 19.5 GiB for an
array with shape (2001, 436747, 3) and data type float64  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 19.5 GiB for an
array with shape (2001, 436747, 3) and data type float64  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 33, in read_coords  
coords = array(coords_list, dtype=float64)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> 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 "C:\Users\kpzj160\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme  
self.openFile()  
File "C:\Users\kpzj160\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 "C:\Users\kpzj160\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 Core Profile Context 23.20.40.01.231124
OpenGL renderer: AMD Radeon(TM) 740M
OpenGL vendor: ATI Technologies Inc.

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

Manufacturer: LENOVO
Model: 21F9S0NX1X
OS: Microsoft Windows 11 Enterprise (Build 22621)
Memory: 15,801,827,328
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 PRO 7540U w/ Radeon 740M Graphics  
OSLanguage: en-US

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
    grako: 3.16.5
    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
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    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: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1
File attachment: 1ao7.pdb

1ao7.pdb

Attachments (1)

1ao7.pdb (516.5 KB ) - added by jhmvangils@… 11 months ago.: Added by email2trac

Download all attachments as: .zip

Change History (4)

by jhmvangils@…, 11 months ago

Attachment:	1ao7.pdb added

Added by email2trac

comment:1 by pett, 11 months ago

Component:	Unassigned → MD/Ensemble Analysis
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Viewing Gromacs output

comment:2 by pett, 11 months ago

Hi,

The Molecular Dynamics Viewer only handles multi-MODEL PDB files. To view Gromacs output, you would first open a PDB file of the simulated system ("open blah.pdb") and then open the corresponding xtc or trr file ("open blah.xtc" or "open blah.trr"). That will bring up a playback interface.
The file you attached (1ao7.pdb) doesn't seem like it would be appropriate as the PDB file for the simulated system since it lacks hydrogen atoms and I assume the simulation includes hydrogens.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by pett, 11 months ago

Resolution:	→ not a bug
Status:	accepted → closed

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