![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Last modified 3 years ago
#8131 feedback defect
SDF charge Index out of bounds
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202212010831 (2022-12-01 08:31:51 UTC)
Description
Opened attached SDF. This ran ok in Chimera, so want to see what's up
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.dev202212010831 (2022-12-01)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip available: 22.2.2 -> 22.3.1
[notice] To update, run: C:\Program Files\ChimeraX_daily\bin\ChimeraX.exe -m
pip install --upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Collecting ChimeraX-NIHPresets==1.1.7
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxnihpresets/releases/1.1.7/ChimeraX_NIHPresets-1.1.7-py3-none-
any.whl (7.1 kB)
Installing collected packages: ChimeraX-NIHPresets
Attempting uninstall: ChimeraX-NIHPresets
Found existing installation: ChimeraX-NIHPresets 1.1.6
Uninstalling ChimeraX-NIHPresets-1.1.6:
Successfully uninstalled ChimeraX-NIHPresets-1.1.6
Successfully installed ChimeraX-NIHPresets-1.1.7
\---
Successfully installed ChimeraX-NIHPresets-1.1.7
Installed ChimeraX-NIHPresets (1.1.7)
> open "C:/Users/brownekm/Downloads/Furfural aminoguanidine bicarbonate.sdf"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX_daily\bin\lib\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 "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 460, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 431, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\sdf\\__init__.py", line 25, in open
return read_sdf(session, data, file_name, **kw)
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\sdf\sdf.py", line 37, in read_sdf
parse_v2000(session, file_name, lines, structures, auto_style)
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\sdf\sdf.py", line 128, in parse_v2000
state, reading_data, indexed_charges, data_name, orig_data_name =
read_data_line(s, state,
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\sdf\sdf.py", line 279, in read_data_line
atoms[index].charge = charge
IndexError: list index out of range
IndexError: list index out of range
File "C:\Program Files\ChimeraX_daily\bin\lib\site-
packages\chimerax\sdf\sdf.py", line 279, in read_data_line
atoms[index].charge = charge
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 466.47
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: HP
Model: HP Z4 G4 Workstation
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 137,220,087,808
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.2.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.5.7
ChimeraX-AddH: 2.2.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.8
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.43.4
ChimeraX-AtomicLibrary: 8.0.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.dev202212010831
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.9
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.7
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-NIHPresets: 1.1.7
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.3
ChimeraX-PDB: 2.6.9
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.4
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.25.2
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.6
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
File attachment: Furfural aminoguanidine bicarbonate.sdf
Attachments (7)
Change History (12)
by , 3 years ago
| Attachment: | Furfural aminoguanidine bicarbonate.sdf added |
|---|
comment:1 by , 3 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → SDF charge Index out of bounds |
comment:3 by , 3 years ago
Where did this file come from? In its PUBCHEM_MMFF94_PARTIAL_CHARGES section it has carriage return characters instead of newline characters.
comment:4 by , 3 years ago
Eric:
It was a user upload, unsure where they got it from. We have 6 of them in the database like this. They somehow ran on 3DPX in Chimera, but they don't open now. Phil could open them in pymol.
Phil would like to discuss in the meeting tomorrow.
I've attached all the files in question just in case.
K
-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, December 6, 2022 4:22 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #8131: SDF charge Index out of bounds
#8131: SDF charge Index out of bounds
---------------------------------------+----------------------
Reporter: kristen.browne@... | Owner: pett
Type: defect | Status: accepted
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------------+----------------------
Comment (by pett):
Where did this file come from? In its PUBCHEM_MMFF94_PARTIAL_CHARGES section it has carriage return characters instead of newline characters.
--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8131%23comment%3A3&data=05%7C01%7Ckristen.browne%40nih.gov%7Cb71cadd352484196f60908dad7cffce3%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638059585543371259%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VRbcD7z1cC00sOnLSaUaOAEHmLmg1G2ca6MdZ4BX82o%3D&reserved=0>
ChimeraX <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C01%7Ckristen.browne%40nih.gov%7Cb71cadd352484196f60908dad7cffce3%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638059585543371259%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OSAXwL6tvaGOQFRznh7cmXIJ4EloTAODoBgQw0UJJ%2FU%3D&reserved=0>
ChimeraX Issue Tracker
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
Furfural aminoguanidine bicarbonate (1).sdf
6-Nitro-2-pyridinecarboxaldehyde aminoguanidine bicarbonate.sdf
5-Nitro-2-thiophenecarboxaldehyde aminoguanidine bicarbonate_0.sdf
5-Nitro-2-thiophenecarboxaldehyde aminoguanidine bicarbonate_0_0.sdf
by , 3 years ago
| Attachment: | 6-Nitro-2-pyridinecarboxaldehyde aminoguanidine bicarbonate.sdf added |
|---|
Added by email2trac
by , 3 years ago
| Attachment: | 5-Nitro-2-thiophenecarboxaldehyde aminoguanidine bicarbonate_0.sdf added |
|---|
Added by email2trac
by , 3 years ago
| Attachment: | 5-Nitro-2-thiophenecarboxaldehyde aminoguanidine bicarbonate_0_0.sdf added |
|---|
Added by email2trac
by , 3 years ago
| Attachment: | 5-Methylfurfural aminoguanidine bicarbonate.sdf added |
|---|
Added by email2trac
follow-up: 4 comment:5 by , 3 years ago
| Status: | accepted → feedback |
|---|
Kristen/Phil will query the user as to the origin of these SDF files.
Note:
See TracTickets
for help on using tickets.
Added by email2trac