Opened 10 months ago

Last modified 9 months ago

#16738 assigned defect

SEQCROW: _read_nbo_coeffs: list index out of range

Reported by: ud21003@… 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:        Windows-10-10.0.26100
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Traceback (most recent call last):   File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\open_command\dialog.py", line 334, in _qt_safe     run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""   File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49, in run     results = command.run(text, log=log, return_json=return_json)               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   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:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-packages\SEQCROW\__init__.py", line 712, in open     return open_nbo(            ^^^^^^^^^   File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-packages\SEQCROW\io.py", line 485, in open_nbo     fr = FileReader((path, fmt, None), nbo_name=orbitals)          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-packages\AaronTools\fileIO.py", line 1590, in __init__     self.read_file(   File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-packages\AaronTools\fileIO.py", line 1757, in read_file     self.read_nbo_47(f, nbo_name=nbo_name)   File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-packages\AaronTools\fileIO.py", line 5785, in read_nbo_47     self._read_nbo_coeffs(nbo_name)   File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-packages\AaronTools\fileIO.py", line 5820, in _read_nbo_coeffs     mo_coeff.extend([float(x) for x in lines[j].split()])                                        ~~~~~^^^ IndexError: list index out of range IndexError: list index out of range File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-packages\AaronTools\fileIO.py", line 5820, in _read_nbo_coeffs mo_coeff.extend([float(x) for x in lines[j].split()]) ~~~~~^^^ See log for complete Python traceback. 

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  

> open D:/PhD-work/4-Hyp-work/Calculations/Dispersion-
> effect/M062X/tripeptide/w-disp/opt/pept-
> bond/PO4G_R_exo_full_opt_M062X_COCS.47

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
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:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\\__init__.py", line 712, in open  
return open_nbo(  
^^^^^^^^^  
File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\io.py", line 485, in open_nbo  
fr = FileReader((path, fmt, None), nbo_name=orbitals)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\fileIO.py", line 1590, in __init__  
self.read_file(  
File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\fileIO.py", line 1757, in read_file  
self.read_nbo_47(f, nbo_name=nbo_name)  
File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\fileIO.py", line 5785, in read_nbo_47  
self._read_nbo_coeffs(nbo_name)  
File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\fileIO.py", line 5820, in _read_nbo_coeffs  
mo_coeff.extend([float(x) for x in lines[j].split()])  
~~~~~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\fileIO.py", line 5820, in _read_nbo_coeffs  
mo_coeff.extend([float(x) for x in lines[j].split()])  
~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4314
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

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

Manufacturer: Micro-Star International Co., Ltd.
Model: Modern 14 C13M
OS: Microsoft Windows 11 Home Single Language (Build 26100)
Memory: 16,869,425,152
MaxProcessMemory: 137,438,953,344
CPU: 12 13th Gen Intel(R) Core(TM) i7-1355U
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
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    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
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    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
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    ChimeraX-MMTF: 2.2
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    ChimeraX-PDBImages: 1.2
    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
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    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
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    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
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    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
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    decorator: 5.1.1
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    executing: 2.0.1
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    ipykernel: 6.29.2
    ipython: 8.21.0
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    jedi: 0.19.1
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    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
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Attachments (2)

4R_HyP_endo.37​ (2.1 MB ) - added by UD21003@… 10 months ago.
Added by email2trac
4R_HyP_endo.47​ (13.4 MB ) - added by UD21003@… 10 months ago.
Added by email2trac

Change History (9)

comment:1 by Eric Pettersen, 10 months ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SEQCROW: _read_nbo_coeffs: list index out of range

Reported by Ashutosh Joshi

comment:2 by Tony Schaefer, 10 months ago 

 Ashutosh,

Could you send me your .47 and one of the coefficient files (e.g. .37) so I
can take a better look at what the NBO parser is messing up?

Thanks,

Tony

On Thu, Jan 30, 2025 at 11:04 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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>

comment:3 by UD21003@…, 10 months ago 

Hello Tony,

Please find attached the .47 and .37 files.

Thank you

Best Regards
Ashutosh Joshi


On Fri, Jan 31, 2025 at 12:27 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>
>
>
>

4R_HyP_endo.37​

4R_HyP_endo.47​

by UD21003@…, 10 months ago

Attachment: 4R_HyP_endo.37​ added

Added by email2trac

by UD21003@…, 10 months ago

Attachment: 4R_HyP_endo.47​ added

Added by email2trac

comment:4 by Tony Schaefer, 9 months ago 

 Ashutosh,

Thanks for sending the files. I have uploaded a patch to the toolshed. To
update, go to Tools > More Tools... on the ChimeraX menu, then find the
SEQCROW page. You should be able to update and follow the prompts from
there. It looks like the parser was expecting an extra space before and
after each section in the .47 file.

Best,

Tony

On Thu, Jan 30, 2025 at 9:06 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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>
>

comment:5 by UD21003@…, 9 months ago 

Hello Tony,

Thank you for looking into this. However, the error persists. Now, the
error message is different than the previous one. I am including the error
message below for your reference.

------------

KeyError: 'funcs_per_shell'

File
"C:\Users\t2040\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-packages\AaronTools\fileIO.py",
line 5817, in _read_nbo_coeffs
while len(self.other["alpha_coefficients"]) ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^

See log for complete Python traceback.

-------------


Thanks & Regards

Ashutosh Joshi



On Tue, Feb 4, 2025 at 1:56 AM Tony Schaefer <tony.schaefer.chem@gmail.com>
wrote:

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>
>
>
>
>> #16738: SEQCROW: _read_nbo_coeffs: list index out of range
>> ----------------------------------+---------------------------
>>           Reporter:  ud21003@…    |      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 UD21003@…):
>>
>>  * Attachment "4R_HyP_endo.47" added.
>>
>>  Added by email2trac
>> --
>> Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16738>
>> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
>> ChimeraX Issue Tracker
>>
>

comment:6 by Tony Schaefer, 9 months ago 

 Ashutosh,

Is this with the two files you sent previously? I am able to open those
without issue. If this is with different files, can you please send those.

Thanks,

Tony

On Tue, Feb 4, 2025 at 1:47 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
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comment:7 by UD21003@…, 9 months ago 

Hello Tony,

First, I tried to open other files and then these two files. Both the
times, I was getting the same error mentioned today's email.

Thank you

Best regards
Ashutosh Joshi

On Tue, 4 Feb, 2025, 20:59 ChimeraX, <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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