![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Last modified 3 years ago
#8114 assigned defect
read_xyz: elements: list index out of range
| Reported by: | Owned by: | Tony Schaefer | |
|---|---|---|---|
| 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-5.15.0-52-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.4rc202205111743 (2022-05-11 17:43:38 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4rc202205111743 (2022-05-11)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/harding/dev/chimerax/CC_50ms_res.xyz
Summary of feedback from opening /home/harding/dev/chimerax/CC_50ms_res.xyz
---
error | unable to open CC_50ms_res.xyz
warnings | WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Ce
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Ce
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Pr
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Ce
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Pr
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Nd
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Ce
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Pr
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Nd
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Pm
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Ce
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Pr
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Nd
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Pm
WARNING AaronTools.atoms.Atom._set_vdw
VDW Radii not found for element: Sm
60 messages similar to the above omitted
Traceback (most recent call last):
File "/home/harding/.local/share/ChimeraX/1.4/site-
packages/AaronTools/fileIO.py", line 1309, in read_xyz
int(line)
ValueError: invalid literal for int() with base 10: '120 1 2190096.00000'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open
return remember_data_format()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File "/home/harding/.local/share/ChimeraX/1.4/site-
packages/SEQCROW/__init__.py", line 482, in open
return open_aarontools(
File "/home/harding/.local/share/ChimeraX/1.4/site-packages/SEQCROW/io.py",
line 40, in open_aarontools
raise e
File "/home/harding/.local/share/ChimeraX/1.4/site-packages/SEQCROW/io.py",
line 32, in open_aarontools
fr = FileReader(
File "/home/harding/.local/share/ChimeraX/1.4/site-
packages/AaronTools/fileIO.py", line 1171, in __init__
self.read_xyz(f, get_all)
File "/home/harding/.local/share/ChimeraX/1.4/site-
packages/AaronTools/fileIO.py", line 1320, in read_xyz
self.atoms += [Atom(element=line[0], coords=line[1:4], name=str(atom_count))]
File "/home/harding/.local/share/ChimeraX/1.4/site-
packages/AaronTools/atoms.py", line 111, in __init__
element = ELEMENTS[int(element)]
IndexError: list index out of range
IndexError: list index out of range
File "/home/harding/.local/share/ChimeraX/1.4/site-
packages/AaronTools/atoms.py", line 111, in __init__
element = ELEMENTS[int(element)]
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 515.43.04
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=Unity
DISPLAY=:1
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen 9 5950X 16-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 10Gi 82Gi 363Mi 32Gi 113Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
09:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:24b0] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:14ad]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4rc202205111743
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.2
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
distro: 1.6.0
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
MolecularDynamicsViewer: 1.4
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 22.3.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
Send2Trash: 1.8.0
SEQCROW: 1.5.10
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.2.0
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → read_xyz: elements: list index out of range |
follow-up: 2 comment:2 by , 3 years ago
Ben,
This will be difficult to diagnose without a bit more information. If you can, please send a file that can reproduce this error.
It looks like it's getting caught on a line in your file that is just '120 1 2190096.00000'. Maybe that's supposed to be a comment? I'm not sure how else that could be interpreted. We support basic XYZ files with the number of atoms on the first line, comment on the next line, followed by the atoms and their coordinates. This pattern can be repeated for XYZ trajectories or different structures.
Here's an example of and XYZ file for benzene:
```
12
benzene
C -1.976956 -2.327177 0.001258
C -2.368139 -1.295544 0.855179
C -1.671361 -0.087354 0.854401
C -0.582097 0.089190 0.000262
C -0.190773 -0.942409 -0.853088
C -0.888480 -2.150555 -0.852891
H -3.226790 -1.434829 1.527903
H -1.980024 0.726060 1.526994
H 0.667658 -0.803584 -1.526362
H -0.579922 -2.963602 -1.525852
H -0.037665 1.033485 -0.000129
H -2.521911 -3.271171 0.001704
```
Here's an XYZ file for part of a molecular dynamics simulation:
```
8
C 0.802100 0.705542 0.037485
C 0.758438 -0.685909 -0.029681
C -0.779628 -0.689902 0.015414
C -0.787136 0.660279 -0.025286
H 1.566553 1.534059 -0.049416
H 1.523200 -1.479421 0.009394
H -1.550881 -1.483313 0.074695
H -1.465573 1.547442 -0.011531
8
C 0.803977 0.705833 0.039085
C 0.760560 -0.684762 -0.032730
C -0.780851 -0.692040 0.016688
C -0.786197 0.658108 -0.026205
H 1.545836 1.533552 -0.046256
H 1.503494 -1.477399 0.018189
H -1.549796 -1.464871 0.079166
H -1.470470 1.561656 -0.014938
8
C 0.806001 0.706018 0.040674
C 0.762664 -0.683450 -0.035765
C -0.782114 -0.694121 0.017940
C -0.785367 0.655899 -0.027108
H 1.524492 1.532986 -0.043140
H 1.483828 -1.475706 0.027076
H -1.548525 -1.446643 0.083636
H -1.474749 1.575554 -0.018352
```
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, December 2, 2022 3:22 PM
Cc: bdharding@wisc.edu <bdharding@wisc.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #8114: read_xyz: elements: list index out of range (was: ChimeraX bug report submission)
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#8114: read_xyz: elements: list index out of range
----------------------------------+---------------------------
Reporter: bdharding@… | Owner: Tony Schaefer
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+---------------------------
Changes (by pett):
* status: new => assigned
* component: Unassigned => Third Party
* project: => ChimeraX
* platform: => all
* owner: (none) => Tony Schaefer
Comment:
Reported by Ben Harding
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8114#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
Note:
See TracTickets
for help on using tickets.
Reported by Ben Harding