Read ORCA: could not broadcast input array

[andreapellegrini6698@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Trying to open an ORCA output, but cat do


Log:
> setattr a radius 1

Assigning radius attribute to 0 items  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/andrea/Desktop/scratch/berny_berny_cis.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/berny_berny_cis.out  
---  
error | unable to open berny_berny_cis.out  
  

Failed opening file /Users/andrea/Desktop/scratch/berny_berny_cis.out:  
could not broadcast input array from shape (0,) into shape (3,)  

> open /Users/andrea/Desktop/scratch/berny_berny_cis.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/berny_berny_cis.out  
---  
error | unable to open berny_berny_cis.out  
  

Failed opening file /Users/andrea/Desktop/scratch/berny_berny_cis.out:  
could not broadcast input array from shape (0,) into shape (3,)  

> open /Users/andrea/Desktop/scratch/berny_berny_cis.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/berny_berny_cis.out  
---  
error | unable to open berny_berny_cis.out  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/__init__.py", line 580, in open  
return open_aarontools(  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/io.py", line 57, in open_aarontools  
raise e  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/io.py", line 34, in open_aarontools  
fr = FileReader(  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/AaronTools/fileIO.py", line 1548, in __init__  
self.read_orca_out(f, get_all, just_geom)  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/AaronTools/fileIO.py", line 2362, in read_orca_out  
gradient[i] = np.array([float(x) for x in info[3:]])  
ValueError: could not broadcast input array from shape (0,) into shape (3,)  
  
ValueError: could not broadcast input array from shape (0,) into shape (3,)  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/AaronTools/fileIO.py", line 2362, in read_orca_out  
gradient[i] = np.array([float(x) for x in info[3:]])  
  
See log for complete Python traceback.  
  

> close




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGP3T/A
      Chip: Unknown
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.60.55
      OS Loader Version: 10151.60.55

Software:

    System Software Overview:

      System Version: macOS 14.2 (23C5041e)
      Kernel Version: Darwin 23.2.0
      Time since boot: 5 days, 17 hours, 49 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        E24-29:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    argcomplete: 3.0.5
    asttokens: 2.2.1
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    Babel: 2.12.1
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    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
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    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
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    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-DistMonitor: 1.4
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    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
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    ChimeraX-Help: 1.2.1
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[Eric Pettersen]

Reported by Andrea Pellegrini

[Tony Schaefer]

Andrea,

Thanks for reporting this, but I'm not exactly sure how to reproduce this.
It looks like our file parser is expecting a different format for the
energy gradient. We've only tested with orca 4.2 and 5.0 output files using
the default output settings for the most part. Could you please send either
the output file, or your input file and the version of orca you're using.
If you don't want to include your structure in the input file, that's fine.

Best,

Tony

On Thu, Nov 16, 2023 at 1:48 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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