SEQCROW: ORCA 5.04 .log output: list index out of range

[j.f.c.turner@…]

The following bug report has been submitted:
Platform:        Linux-6.8.11-200.fc39.x86_64-x86_64-with-glibc2.38
ChimeraX Version: 1.8rc202406102315 (2024-06-10 23:15:52 UTC)
Description
Attempted to open an ORCA 5.04 .log output file

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: 1.8rc202406102315 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle SEQCROW-1.8.8-py3-none-any.whl  
Installed SEQCROW (1.8.8)  

> open
> /home/jturner/calculations/orca/organic/jw_pyrrole/jw_pyrrole_yne_diester_opt.log

Summary of feedback from opening
/home/jturner/calculations/orca/organic/jw_pyrrole/jw_pyrrole_yne_diester_opt.log  
---  
error | unable to open jw_pyrrole_yne_diester_opt.log  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/jturner/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/__init__.py", line 567, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "/home/jturner/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/io.py", line 46, in open_aarontools  
raise e  
File "/home/jturner/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/io.py", line 34, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "/home/jturner/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/fileIO.py", line 1544, in __init__  
self.read_log(f, get_all, just_geom, scan_read_all)  
File "/home/jturner/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/fileIO.py", line 3690, in read_log  
route += line[1:].splitlines()[0]  
~~~~~~~~~~~~~~~~~~~~~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/home/jturner/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/fileIO.py", line 3690, in read_log  
route += line[1:].splitlines()[0]  
~~~~~~~~~~~~~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.3.6
OpenGL renderer: Mesa Intel(R) Graphics (RPL-P)
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=xfce
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: Dell Inc.
Model: XPS 15 9530
OS: Fedora Linux 39 Workstation Edition
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 13th Gen Intel(R) Core(TM) i7-13700H
Cache Size: 24576 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       7.5Gi       1.3Gi       1.7Gi        56Gi        54Gi
	Swap:          8.0Gi       3.5Mi       8.0Gi

Graphics:
	0000:00:02.0 VGA compatible controller [0300]: Intel Corporation Raptor Lake-P [Iris Xe Graphics] [8086:a7a0] (rev 04)	
	Subsystem: Dell Device [1028:0beb]	
	Kernel driver in use: i915

Installed Packages:
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    appdirs: 1.4.4
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    blosc2: 2.0.0
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    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
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    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-BasicActions: 1.1.2
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    ChimeraX-BlastProtein: 2.4.6
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    ChimeraX-BugReporter: 1.0.1
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    ChimeraX-ConnectStructure: 2.0.1
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    ChimeraX-Crystal: 1.0
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    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
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    ChimeraX-Hbonds: 2.4
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    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
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    ChimeraX-vrml: 1.0
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    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
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    colorama: 0.4.6
    comm: 0.2.2
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    Cython: 3.0.10
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    setuptools: 69.5.1
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    tzdata: 2024.1
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    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
File attachment: jw_pyrrole_direct_complex_opt.log

jw_pyrrole_direct_complex_opt.log​

[j.f.c.turner@…]

Added by email2trac

[Eric Pettersen]

Reported by John Turner

[Tony Schaefer]

John,

Orca files are expected to have a .out extension instead of .log. I don't
think there's a set standard for orca file extensions, but from what I've
seen in the orca documentation and tutorials .out seems the most common.
You can run `open /path/to/your_file_here.log format out` to override the
inferred format, or you can rename the file. I renamed the file you
supplied and was able to open it. With .log, the parser is expecting a
Gaussian output file.

Best,

Tony

On Wed, Jun 12, 2024 at 11:45 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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