SEQCROW: NMR Spectrum: list index out of range

[t.swift@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
I am using ORCA 5 - and nearing the end of a very long study - so I am resistant to upgrading to ORCA 6 until the current workplan is finished. I did note however that in the new manuals they advertise that ChimeraX can be used to visualise ORCA outputs - and I tried this and indeed - it can load and display propeties from my calculations.
I want to load my NMR calculations - conducted in ORCA 5
(typical input line looks like this:
-----------------
!B3LYP PCSSEG-2 AUTOAUX NMR CPCM(CHLOROFORM)
* xyz 0 1
H -1.36375 -2.14710 -0.00000
C -0.81841 -1.20707 -0.00000
C 0.57773 -1.21178 0.00000
H 1.10440 -2.16317 0.00000
C 1.29013 -0.00662 0.00000
C 2.78990 0.00393 0.00000
C 0.58296 1.20255 0.00000
H 1.11797 2.14948 0.00000
C -0.81284 1.20580 -0.00000
H -1.35324 2.14861 -0.00000
C -1.51325 0.00108 -0.00000
H -2.59986 0.00360 -0.00000
H 3.19906 -1.01171 -0.00000
H 3.16332 0.51620 0.89251
H 3.16332 0.51620 -0.89251
*
%EPRNMR
NUCLEI = ALL H {SHIFT, SSALL}
END
---------------
and it does produce an output file with reasonable NMR information I can manually extract with reasonable peak predictions.
But when it comes to creating a visualised spectra (which is what I really need) I am still looking for a solution. I had hoped ChimeraX would work - so I downloaded and installed it, added the SEQCROW plugin, and opened my output file. However it produces error messages whenever I try to open the output files
Here are the logs showing typical errors. Error 1) error that it wants me to use electronic energy (or rather - it demands I provide a frequency job. How am imeant to do this?) I then manually change the energy for weighting to electronic and click on plot and I now get Error 2) IndexError: list index out of range
Here is the full log display of that process:
open "Y:/Papers/Refaat/L Proline/Structures/5 NMR/Toluene.out"Opened Toluene.out as an ORCA output file
ui tool show "NMR Spectrum"frequency jobs must be given if you are not weighting based on electronic energy
NRG
Traceback (most recent call last):
  File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-packages\SEQCROW\tools\nmr_plot.py", line 458, in <lambda>
tabs.currentChanged.connect(lambda ndx: self.refresh_plot() if ndx == 2 else None)
^^^^^^^^^^^^^^^^^^^
  File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-packages\SEQCROW\tools\nmr_plot.py", line 1460, in refresh_plot
mixed_spectra = self.get_mixed_spectrum()
^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-packages\SEQCROW\tools\nmr_plot.py", line 1304, in get_mixed_spectrum
conf_mixed = NMR.get_mixed_signals(
^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-packages\AaronTools\spectra.py", line 2361, in get_mixed_signals
out = cls(new_data, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-packages\AaronTools\spectra.py", line 2219, in __init__
super().__init__(*args, **kwargs)
  File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-packages\AaronTools\spectra.py", line 73, in __init__
if isinstance(data[0], Signal):
~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-packages\AaronTools\spectra.py", line 73, in __init__
if isinstance(data[0], Signal):
~~~~^^^
See log for complete Python traceback.
----------------
Does anyone have any idea what I'm doing wrong? Is it that I am using ORCA 5 rather than ORCA 6? Is it something in my outputs - am I missing something in my NMR input file (I note that my original tutorial guide for ORCA 5 (NMR spectra - ORCA 5.0 tutorials) used PCSSEG-2 rather than PCSSEG-1 which is used in the ORCA 6 example... Or have i likely mis-installed something in ChimeraX which otherwise seems to work fine for anything that isn't generating a plot.... That IndexError points to a file in the ChimeraX installation which worries me,
Any suggestions would be greatly appreciated

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "Y:\Papers\Refaat\L Proline\Structures\5 NMR\1A.out" format out

Opened 1A.out as an ORCA output file  

> ui tool show "NMR Spectrum"

frequency jobs must be given if you are not weighting based on electronic
energy  
NRG  
Traceback (most recent call last):  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 458, in <lambda>  
tabs.currentChanged.connect(lambda ndx: self.refresh_plot() if ndx == 2 else
None)  
^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 1460, in refresh_plot  
mixed_spectra = self.get_mixed_spectrum()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 1304, in get_mixed_spectrum  
conf_mixed = NMR.get_mixed_signals(  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 2361, in get_mixed_signals  
out = cls(new_data, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 2219, in __init__  
super().__init__(*args, **kwargs)  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 73, in __init__  
if isinstance(data[0], Signal):  
~~~~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 73, in __init__  
if isinstance(data[0], Signal):  
~~~~^^^  
  
See log for complete Python traceback.  
  

> close session

> open "Y:/Papers/Refaat/L Proline/Structures/5 NMR/Toluene.out"

Opened Toluene.out as an ORCA output file  

> ui tool show "NMR Spectrum"

frequency jobs must be given if you are not weighting based on electronic
energy  
NRG  
Traceback (most recent call last):  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 458, in <lambda>  
tabs.currentChanged.connect(lambda ndx: self.refresh_plot() if ndx == 2 else
None)  
^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 1460, in refresh_plot  
mixed_spectra = self.get_mixed_spectrum()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 1304, in get_mixed_spectrum  
conf_mixed = NMR.get_mixed_signals(  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 2361, in get_mixed_signals  
out = cls(new_data, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 2219, in __init__  
super().__init__(*args, **kwargs)  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 73, in __init__  
if isinstance(data[0], Signal):  
~~~~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 73, in __init__  
if isinstance(data[0], Signal):  
~~~~^^^  
  
See log for complete Python traceback.  
  
RRHO  
NRG  
Traceback (most recent call last):  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 458, in <lambda>  
tabs.currentChanged.connect(lambda ndx: self.refresh_plot() if ndx == 2 else
None)  
^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 1460, in refresh_plot  
mixed_spectra = self.get_mixed_spectrum()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 1304, in get_mixed_spectrum  
conf_mixed = NMR.get_mixed_signals(  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 2361, in get_mixed_signals  
out = cls(new_data, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 2219, in __init__  
super().__init__(*args, **kwargs)  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 73, in __init__  
if isinstance(data[0], Signal):  
~~~~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 73, in __init__  
if isinstance(data[0], Signal):  
~~~~^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 458, in <lambda>  
tabs.currentChanged.connect(lambda ndx: self.refresh_plot() if ndx == 2 else
None)  
^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 1460, in refresh_plot  
mixed_spectra = self.get_mixed_spectrum()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\nmr_plot.py", line 1304, in get_mixed_spectrum  
conf_mixed = NMR.get_mixed_signals(  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 2361, in get_mixed_signals  
out = cls(new_data, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 2219, in __init__  
super().__init__(*args, **kwargs)  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 73, in __init__  
if isinstance(data[0], Signal):  
~~~~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Users\tswif\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 73, in __init__  
if isinstance(data[0], Signal):  
~~~~^^^  
  
See log for complete Python traceback.  
  

> ui tool show "AaronTools Fragment Library"




OpenGL version: 3.3.0 NVIDIA 536.48
OpenGL renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Acer
Model: Predator PO5-600s
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 17,090,158,592
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
OSLanguage: en-GB

Installed Packages:
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    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.20
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
File attachment: Toluene.out

Toluene.out​

[t.swift@…]

Added by email2trac

[Eric Pettersen]

Reported by Thomas Swift

[Tony Schaefer]

Thomas,

Thanks for reporting this. It looks like there's some differences in how
orca 5 and 6 print NMR data. There's a line the parser was looking for to
know when to stop reading NMR data, and in this output it is just a couple
lines after it started reading the NMR data. I've done a quick fix for
that, but I'll need to do more testing to make sure this isn't messing with
orca 6 or double hybrid outputs before I update the version on the
toolshed.

In the meantime, you can grab the patch for the plugin on github:
https://github.com/QChASM/SEQCROW?tab=readme-ov-file#github

Best,

Tony

On Tue, Apr 15, 2025 at 10:59 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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