SEQCROW open .out: max() arg is an empty sequence

[tejalsawant.329@…]

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)

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  

> ui tool show "Visualize Normal Modes"

> open "C:/Users/DELL/Downloads/molecule0.g98 (19).out"

Summary of feedback from opening C:/Users/DELL/Downloads/molecule0.g98
(19).out  
---  
notes | molecule0.g98 (19).out has 3 imaginary harmonic vibrational modes  
10293.80i  
9413.33i  
6616.04i  
  
  
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\DELL\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\\__init__.py", line 596, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\io.py", line 110, in open_aarontools  
structure = geom.get_chimera(  
^^^^^^^^^^^^^^^^^  
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\residue_collection.py", line 1016, in get_chimera  
max_disp = max(np.linalg.norm(x) for x in mode.vector)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: max() arg is an empty sequence  
  
ValueError: max() arg is an empty sequence  
  
File "C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\residue_collection.py", line 1016, in get_chimera  
max_disp = max(np.linalg.norm(x) for x in mode.vector)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4624
OpenGL renderer: Intel(R) HD Graphics 5500
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: LENOVO
Model: 80HR
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 8,499,601,408
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-5010U CPU @ 2.10GHz
OSLanguage: en-US

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    ChimeraX-AddCharge: 1.5.17
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[pett]

Reported by Tejal Sawant

ChimeraX 1.8 and SEQCROW 1.8.20

[Tony Schaefer]

Tejal,

Can you send me this file? It looks like it might be a Gaussian 98 file,
which hasn't been tested with the file parser.

Thanks,

Tony

On Mon, Jun 9, 2025 at 12:00 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>
>

[Tony Schaefer]

Tejal,

I've had a chance to look at this, and the issue comes from the large
negative frequencies. I should be able to fix this once I have time. A
temporary workaround would be for you to manually add a space in front of
any frequency that is less than or equal to -10000 (i.e. turn "Frequencies
---10287.5108" to "Frequencies -- -10287.5108"). Some more details on the
issue are below.

It looks like this computation used xtb, which prints the frequencies in
Gaussian format. By default, Gaussian only prints two decimal places for
the normal mode displacements. In Gaussian, you can request more decimal
places to be printed by adding freq=HPModes to your input, but I'm not
aware of a similar setting for xtb. With freq=HPModes, Gaussian will not
just print more decimal places, but print the frequency data in a
completely different format.

One of the main ways our parser knows which format to read is by checking
for freq=HPModes elsewhere in the file. This is not possible in your case
because xtb doesn't print a full Gaussian output, just the structure and
frequency section. The other way is by looking for three consecutive
hyphens (i.e. "---") in the frequency data. The default output normally
only has two consecutive hyphens, however in these examples the first
mode's frequency is < -10000. These get printed like this in the output:
"Frequencies ---10287.5108". The two hyphens next to -10287.5108 make it
look like the three hyphens for the HPModes format, and so it tries to read
HPModes formatted data. Except the data isn't actually in HPModes format,
so it fails for parse the data.

Best,

Tony

On Mon, Jun 9, 2025 at 11:00 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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>
>
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