SEQCROW: ORCA .out: not enough values to unpack

[zhaochen@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here) I can't open diclofenac.out files by using ChimeraX.It shows that not enough values to unpack(expected 3,got 0).

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  

> toolshed show

> open F:/ORCA运行程序/C3H6O-right.out

Summary of feedback from opening F:/ORCA运行程序/C3H6O-right.out  
---  
note | C3H6O-right.out has 0 imaginary harmonic vibrational modes  
  
Opened C3H6O-right.out as an ORCA output file  

> open F:/ORCA运行程序/diclofenac.out

Summary of feedback from opening F:/ORCA运行程序/diclofenac.out  
---  
error | unable to open diclofenac.out as a ORCA output file  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\graphics.py", line 54,
in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\graphics.py", line
124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py", line 697, in
dropEvent  
_open_dropped_file(self.session, p)  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py", line 2075, in
_open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "E:\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 "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\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 "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\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 "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\open_command\cmd.py",
line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "E:\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\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\\__init__.py", line 596, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\io.py", line 45, in open_aarontools  
raise e  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\io.py", line 33, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\fileIO.py", line 1555, in __init__  
self.read_orca_out(f, get_all, just_geom)  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\fileIO.py", line 2568, in read_orca_out  
_, _, rot = line.split()  
^^^^^^^^^  
ValueError: not enough values to unpack (expected 3, got 0)  
  
ValueError: not enough values to unpack (expected 3, got 0)  
  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\fileIO.py", line 2568, in read_orca_out  
_, _, rot = line.split()  
^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 536.23
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: Supermicro
Model: X11DAi-N
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 33,985,892,352
MaxProcessMemory: 137,438,953,344
CPU: 56 Intel(R) Xeon(R) Platinum 8176M CPU @ 2.10GHz
OSLanguage: zh-CN

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
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    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
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    ChimeraX-AlphaFold: 1.0
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    ChimeraX-BILD: 1.0
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    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
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    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
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    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
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    imagecodecs: 2024.1.1
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    ipython: 8.21.0
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    jinja2: 3.1.4
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    python-dateutil: 2.9.0.post0
    pytz: 2024.1
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    Send2Trash: 1.8.3
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    setuptools: 69.5.1
    sfftk-rw: 0.8.1
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    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1
File attachment: diclofenac.out

diclofenac.out​

[zhaochen@…]

Added by email2trac

[Eric Pettersen]

Reported by Zhao Chen

[Tony Schaefer]

Zhao Chen,

Thank you for including an output file. The issue is the parser not
handling VCD data when there are imaginary vibrational frequencies (the
attached file has two imaginary modes). I will fix that in a future update,
however frequency computations should only be done at stationary points.
The harmonic oscillator approximation used to compute the vibrational modes
is only valid at stationary points, and I'm not sure computed spectra for
saddle points makes sense. I'd recommend using the same level of theory to
compute the VCD that you used to optimize the geometry.

Thanks,

Tony

On Sun, Oct 13, 2024 at 6:19 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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