Opened 4 months ago

Last modified 3 months ago

#18295 assigned defect

SEQCROW: trouble reading ORCA output file

Reported by: chimerax-bug-report@… Owned by: Tony Schaefer
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.4-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/tianyizhang98/Library/CloudStorage/GoogleDrive-
> tz6009@princeton.edu/My Drive/Chirik Group/Project 2. P4Fe_C-H_activation/7.
> Computations/High Spin Fe(II)/dcypeFeMeAr/cis-quintet-conf1/cc-re-
> scan_run2/dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.out"

Summary of feedback from opening
/Users/tianyizhang98/Library/CloudStorage/GoogleDrive-tz6009@princeton.edu/My
Drive/Chirik Group/Project 2. P4Fe_C-H_activation/7. Computations/High Spin
Fe(II)/dcypeFeMeAr/cis-quintet-conf1/cc-re-scan_run2/dcypeFeMeAr_cis-quintet-
conf1_cc-re-scan_run2.out  
---  
error | unable to open dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.out as a ORCA output file  
warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out   
an error occured while reading the ORCA output file  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
================================================================================  
  
16 messages similar to the above omitted  
  
Summary of feedback from opening
/Users/tianyizhang98/Library/CloudStorage/GoogleDrive-tz6009@princeton.edu/My
Drive/Chirik Group/Project 2. P4Fe_C-H_activation/7. Computations/High Spin
Fe(II)/dcypeFeMeAr/cis-quintet-conf1/cc-re-scan_run2/dcypeFeMeAr_cis-quintet-
conf1_cc-re-scan_run2.out  
---  
error | unable to open dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.out as a ORCA output file  
  
Summary of feedback from opening
/Users/tianyizhang98/Library/CloudStorage/GoogleDrive-tz6009@princeton.edu/My
Drive/Chirik Group/Project 2. P4Fe_C-H_activation/7. Computations/High Spin
Fe(II)/dcypeFeMeAr/cis-quintet-conf1/cc-re-scan_run2/dcypeFeMeAr_cis-quintet-
conf1_cc-re-scan_run2.out  
---  
error | unable to open dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.out as a ORCA output file  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 731, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2117, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/SEQCROW/__init__.py", line 596,
in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/SEQCROW/io.py", line 42, in
open_aarontools  
raise e  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/SEQCROW/io.py", line 33, in
open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
1632, in __init__  
self.read_orca_out(f, get_all, just_geom, log=None)  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
3222, in read_orca_out  
raise e  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
3207, 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 7429:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 7429:
invalid start byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  

> open "/Users/tianyizhang98/Library/CloudStorage/GoogleDrive-
> tz6009@princeton.edu/My Drive/Chirik Group/Project 2. P4Fe_C-H_activation/7.
> Computations/High Spin Fe(II)/dcypeFeMeAr/cis-quintet-conf1/cc-re-
> scan_run2/dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2_trj.xyz"

opened dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2_trj.xyz as an XYZ
coordinate file movie  

> close

> open "/Users/tianyizhang98/Library/CloudStorage/GoogleDrive-
> tz6009@princeton.edu/My Drive/Chirik Group/Project 2. P4Fe_C-H_activation/7.
> Computations/High Spin Fe(II)/dcypeFeMeAr/cis-quintet-conf1/cc-re-
> scan_run2/dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.out"

Summary of feedback from opening
/Users/tianyizhang98/Library/CloudStorage/GoogleDrive-tz6009@princeton.edu/My
Drive/Chirik Group/Project 2. P4Fe_C-H_activation/7. Computations/High Spin
Fe(II)/dcypeFeMeAr/cis-quintet-conf1/cc-re-scan_run2/dcypeFeMeAr_cis-quintet-
conf1_cc-re-scan_run2.out  
---  
error | unable to open dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.out as a ORCA output file  
warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out   
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
================================================================================  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
NAME = dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.inp  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 1> ! UKS Opt TPSS D4 RIJCOSX UNO UCO DKH-def2-TZVP def2/J def2-TZVP/C  
TightOpt TightSCF  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 2>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 3> %base "dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2"  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 4>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 5> %geom  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 6> Scan  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 7> B 3 7 = 2.447, 1.547, 10 # avogadro numbering is C4 C8  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 8> end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 9> end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 10>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 11> * xyzfile 0 5 last-geom-2447.xyz  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 12>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 13> %pal nprocs 32 end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 14>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
================================================================================  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
NAME = dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.inp  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 1> ! UKS Opt TPSS D4 RIJCOSX UNO UCO DKH-def2-TZVP def2/J def2-TZVP/C  
TightOpt TightSCF  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 2>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 3> %base "dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2"  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 4>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 5> %geom  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 6> Scan  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 7> B 3 7 = 2.447, 1.547, 10 # avogadro numbering is C4 C8  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 8> end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 9> end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 10>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 11> * xyzfile 0 5 last-geom-2447.xyz  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 12>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 13> %pal nprocs 32 end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 14>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
================================================================================  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
NAME = dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.inp  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 1> ! UKS Opt TPSS D4 RIJCOSX UNO UCO DKH-def2-TZVP def2/J def2-TZVP/C  
TightOpt TightSCF  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 2>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 3> %base "dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2"  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 4>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 5> %geom  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 6> Scan  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 7> B 3 7 = 2.447, 1.547, 10 # avogadro numbering is C4 C8  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 8> end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 9> end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 10>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 11> * xyzfile 0 5 last-geom-2447.xyz  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 12>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 13> %pal nprocs 32 end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 14>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
================================================================================  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
NAME = dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.inp  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 1> ! UKS Opt TPSS D4 RIJCOSX UNO UCO DKH-def2-TZVP def2/J def2-TZVP/C  
TightOpt TightSCF  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 2>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 3> %base "dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2"  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 4>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 5> %geom  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 6> Scan  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 7> B 3 7 = 2.447, 1.547, 10 # avogadro numbering is C4 C8  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 8> end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 9> end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 10>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 11> * xyzfile 0 5 last-geom-2447.xyz  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 12>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 13> %pal nprocs 32 end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 14>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
================================================================================  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
NAME = dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.inp  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 1> ! UKS Opt TPSS D4 RIJCOSX UNO UCO DKH-def2-TZVP def2/J def2-TZVP/C  
TightOpt TightSCF  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 2>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 3> %base "dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2"  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 4>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 5> %geom  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 6> Scan  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 7> B 3 7 = 2.447, 1.547, 10 # avogadro numbering is C4 C8  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 8> end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 9> end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 10>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 11> * xyzfile 0 5 last-geom-2447.xyz  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 12>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 13> %pal nprocs 32 end  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
| 14>  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: 708. D(C 61,C 69,C 66,H 70) 64.58 -0.000101  
0.36 64.94  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: opt_steps, charge, multiplicity, n_basis,  
scf_energy, n_alpha, n_beta, Mulliken Charges, Löwdin Charges, Mulliken  
gross atomic population, Total nuclear charge, Mulliken gross atomic charge,  
Mayer's total valence, Mayer's bonded valence, Mayer's free valence,  
dispersion correction energy, energy, forces, gradient,  
rotational_temperature, error  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
================================================================================  
  
16 messages similar to the above omitted  
  
Summary of feedback from opening
/Users/tianyizhang98/Library/CloudStorage/GoogleDrive-tz6009@princeton.edu/My
Drive/Chirik Group/Project 2. P4Fe_C-H_activation/7. Computations/High Spin
Fe(II)/dcypeFeMeAr/cis-quintet-conf1/cc-re-scan_run2/dcypeFeMeAr_cis-quintet-
conf1_cc-re-scan_run2.out  
---  
error | unable to open dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.out as a ORCA output file  
  
Summary of feedback from opening
/Users/tianyizhang98/Library/CloudStorage/GoogleDrive-tz6009@princeton.edu/My
Drive/Chirik Group/Project 2. P4Fe_C-H_activation/7. Computations/High Spin
Fe(II)/dcypeFeMeAr/cis-quintet-conf1/cc-re-scan_run2/dcypeFeMeAr_cis-quintet-
conf1_cc-re-scan_run2.out  
---  
error | unable to open dcypeFeMeAr_cis-quintet-conf1_cc-re-scan_run2.out as a ORCA output file  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 731, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2117, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/SEQCROW/__init__.py", line 596,
in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/SEQCROW/io.py", line 42, in
open_aarontools  
raise e  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/SEQCROW/io.py", line 33, in
open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
1632, in __init__  
self.read_orca_out(f, get_all, just_geom, log=None)  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
3222, in read_orca_out  
raise e  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
3207, 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 7429:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 7429:
invalid start byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 7459.121.3
      OS Loader Version: 7459.121.3

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 23:11

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP 27f:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.20
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by Eric Pettersen, 4 months ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SEQCROW: trouble reading ORCA output file

comment:2 by Tony Schaefer, 3 months ago 

I'm not exactly sure what's going on. I added some more debug prints in the
more recent versions, so at least there's some info. It looks like the
parser grabbed quite a bit of info before hitting a UnicodeDecodeError. I'd
expect to encounter a UnicodeDecodeError a lot earlier. Unless something
weird is going on, the line after the last one it reads is either basically
identical to this (printing some dihedral angle) or a bunch of hyphens.
With all the info that's been parsed already, orca should have already
printed a similar line, at the very least, when it reprints the input
structure for this optimization job. My best guess is something is wrong
with the file, but I can't be sure without access to the file.

On Mon, Jul 28, 2025 at 12:04 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
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