SDF charge Index out of bounds

[kristen.browne@…]

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
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    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
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    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
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    ChimeraX-StdCommands: 1.10.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
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    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.4
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
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    ChimeraX-UI: 1.25.2
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    ChimeraX-UnitCell: 1.0.1
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    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
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    colorama: 0.4.5
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    wcwidth: 0.2.5
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File attachment: Furfural aminoguanidine bicarbonate.sdf

Furfural aminoguanidine bicarbonate.sdf​

[kristen.browne@…]

Added by email2trac

[pett]

This file does not open in Chimera either.

[pett]

Where did this file come from? In its PUBCHEM_MMFF94_PARTIAL_CHARGES section it has carriage return characters instead of newline characters.

[kristen.browne@…]

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.

--
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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​

5-Methylfurfural aminoguanidine bicarbonate.sdf​

Conformer3D_CID_443589_1.sdf​

[kristen.browne@…]

Added by email2trac

[kristen.browne@…]

Added by email2trac

[kristen.browne@…]

Added by email2trac

[kristen.browne@…]

Added by email2trac

[kristen.browne@…]

Added by email2trac

[kristen.browne@…]

Added by email2trac

[pett]

Kristen/Phil will query the user as to the origin of these SDF files.