SEQCROW: unable to open orca.out as a ORCA output file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/User/Downloads/Kiomputasi Kuantum/TSetilasetat.out"

Unrecognized file suffix '.out'  

> open "C:/Users/User/Downloads/Pembentukan Garam/Orca6-1/reak3152/orca.out"

Unrecognized file suffix '.out'  

> toolshed show

Downloading bundle seqcrow-1.8.21-py3-none-any.whl  
Installed SEQCROW (1.8.21)  

> ui tool show "Visualize Normal Modes"

> open "C:/Users/User/Downloads/Pembentukan Garam/Orca6-1/reak3152/orca.out"

Summary of feedback from opening C:/Users/User/Downloads/Pembentukan
Garam/Orca6-1/reak3152/orca.out  
---  
error | unable to open orca.out as a ORCA output file  
  
Summary of feedback from opening C:/Users/User/Downloads/Pembentukan
Garam/Orca6-1/reak3152/orca.out  
---  
note | orca.out has 0 imaginary harmonic vibrational modes  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\\__init__.py", line 596, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\io.py", line 42, in open_aarontools  
raise e  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\io.py", line 33, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\AaronTools\fileIO.py", line 1632, in __init__  
self.read_orca_out(f, get_all, just_geom, log=None)  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\AaronTools\fileIO.py", line 2413, in read_orca_out  
line = f.readline()  
^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0:
invalid start byte  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 339, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.10.1\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 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 225, in provider_open  
models, status = collated_open(session, None, [data], data_format,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\\__init__.py", line 596, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\io.py", line 110, in open_aarontools  
structure = geom.get_chimera(  
^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\residue_collection.py", line 1006, in get_chimera  
xyzs = self.all_geom_coordsets(filereader)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\residue_collection.py", line 979, in all_geom_coordsets  
coordsets[i][j] = atom.coords  
~~~~~~~~~~~~^^^  
IndexError: index 11 is out of bounds for axis 0 with size 11  
  
IndexError: index 11 is out of bounds for axis 0 with size 11  
  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\residue_collection.py", line 979, in all_geom_coordsets  
coordsets[i][j] = atom.coords  
~~~~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  

> open "C:/Users/User/Downloads/Pembentukan Garam/Orca6-1/reak3152/orca.out"

Summary of feedback from opening C:/Users/User/Downloads/Pembentukan
Garam/Orca6-1/reak3152/orca.out  
---  
error | unable to open orca.out as a ORCA output file  
  
Summary of feedback from opening C:/Users/User/Downloads/Pembentukan
Garam/Orca6-1/reak3152/orca.out  
---  
note | orca.out has 0 imaginary harmonic vibrational modes  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\\__init__.py", line 596, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\io.py", line 42, in open_aarontools  
raise e  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\io.py", line 33, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\AaronTools\fileIO.py", line 1632, in __init__  
self.read_orca_out(f, get_all, just_geom, log=None)  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\AaronTools\fileIO.py", line 2413, in read_orca_out  
line = f.readline()  
^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0:
invalid start byte  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 339, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.10.1\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 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 225, in provider_open  
models, status = collated_open(session, None, [data], data_format,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\\__init__.py", line 596, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\io.py", line 110, in open_aarontools  
structure = geom.get_chimera(  
^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\residue_collection.py", line 1006, in get_chimera  
xyzs = self.all_geom_coordsets(filereader)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\residue_collection.py", line 979, in all_geom_coordsets  
coordsets[i][j] = atom.coords  
~~~~~~~~~~~~^^^  
IndexError: index 11 is out of bounds for axis 0 with size 11  
  
IndexError: index 11 is out of bounds for axis 0 with size 11  
  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\SEQCROW\residue_collection.py", line 979, in all_geom_coordsets  
coordsets[i][j] = atom.coords  
~~~~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 451.67
OpenGL renderer: GeForce 930MX/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: id_ID.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: X456URK
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 21,349,564,416
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
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    ChimeraX-AlignmentMatrices: 2.1
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    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.21
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

[Tony Schaefer]

These are typically pretty challenging to diagnose without the file at
hand. A new version of orca released a couple weeks ago, and it looks like
this user is probably using that. I didn't think they'd change how
coordinates are printed, but I'll play around with it and see if I find any
issues.

On Fri, Jul 25, 2025 at 12:50 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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