SEQCROW: trouble reading ORCA output file

[tz6009@…]

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Unable to open this ORCA output file using ChimeraX. Most of times this type of files can be opened with no problem, but this one was problematic due to a "python error" which pops up when I drag it into ChimeraX.

Log:
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/Princeton Dropbox/Tianyi
> Zhang/Computations/Borylation
> Computation/(ACNC)Fe/iPrACNCFeNs2N2/singlet/opt/iPrACNCFeNs2N2_singlet_opt_tpss-
> tzvp.out"

Summary of feedback from opening /Users/tianyizhang98/Princeton Dropbox/Tianyi
Zhang/Computations/Borylation
Computation/(ACNC)Fe/iPrACNCFeNs2N2/singlet/opt/iPrACNCFeNs2N2_singlet_opt_tpss-
tzvp.out  
---  
notes | iPrACNCFeNs2N2_singlet_opt_tpss-tzvp.out has 3 imaginary harmonic vibrational modes  
435.97i  
127.00i  
44.44i  
  
  
Opened iPrACNCFeNs2N2_singlet_opt_tpss-tzvp.out as an ORCA output file  

> ui tool show "Visualize Normal Modes"

> hide target m

> close

> open "/Users/tianyizhang98/Princeton Dropbox/Tianyi
> Zhang/Computations/Borylation
> Computation/(ACNC)Fe/iPrACNCFeNs2N2/triplet/opt/iPrACNCFeNs2N2_triplet_opt_tpss-
> tzvp.out"

Summary of feedback from opening /Users/tianyizhang98/Princeton Dropbox/Tianyi
Zhang/Computations/Borylation
Computation/(ACNC)Fe/iPrACNCFeNs2N2/triplet/opt/iPrACNCFeNs2N2_triplet_opt_tpss-
tzvp.out  
---  
note | iPrACNCFeNs2N2_triplet_opt_tpss-tzvp.out has 0 imaginary harmonic vibrational modes  
  
Opened iPrACNCFeNs2N2_triplet_opt_tpss-tzvp.out as an ORCA output file  

> ui tool show "Visualize Normal Modes"

> open "/Users/tianyizhang98/Princeton Dropbox/Tianyi
> Zhang/Computations/Borylation
> Computation/(ACNC)Fe/iPrACNCFeNs2N2/singlet/opt/iPrACNCFeNs2N2_singlet_opt_tpss-
> tzvp.out"

Summary of feedback from opening /Users/tianyizhang98/Princeton Dropbox/Tianyi
Zhang/Computations/Borylation
Computation/(ACNC)Fe/iPrACNCFeNs2N2/singlet/opt/iPrACNCFeNs2N2_singlet_opt_tpss-
tzvp.out  
---  
notes | iPrACNCFeNs2N2_singlet_opt_tpss-tzvp.out has 3 imaginary harmonic vibrational modes  
435.97i  
127.00i  
44.44i  
  
  
Opened iPrACNCFeNs2N2_singlet_opt_tpss-tzvp.out as an ORCA output file  

> close

> open "/Users/tianyizhang98/Princeton Dropbox/Tianyi
> Zhang/Computations/Borylation
> Computation/(ACNC)Fe/iPrACNCFeBPin2/singlet/opt/iPrACNCFeBpin2_singlet_opt_tpss-
> tzvp.out"

Summary of feedback from opening /Users/tianyizhang98/Princeton Dropbox/Tianyi
Zhang/Computations/Borylation
Computation/(ACNC)Fe/iPrACNCFeBPin2/singlet/opt/iPrACNCFeBpin2_singlet_opt_tpss-
tzvp.out  
---  
error | unable to open iPrACNCFeBpin2_singlet_opt_tpss-tzvp.out as a ORCA output file  
warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out   
  
error while reading ORCA gradient  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
an error occured while reading the ORCA output file  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
  
2 messages similar to the above omitted  
  
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 605,
in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/SEQCROW/io.py", line 46, 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
1634, 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
3280, in read_orca_out  
raise e  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2720, in read_orca_out  
raise e  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2712, in read_orca_out  
gradient.append([float(x) for x in info[3:]])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2712, in <listcomp>  
gradient.append([float(x) for x in info[3:]])  
^^^^^^^^  
ValueError: could not convert string to float: '0.0Starting'  
  
ValueError: could not convert string to float: '0.0Starting'  
  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2712, in  
gradient.append([float(x) for x in info[3:]])  
^^^^^^^^  
  
See log for complete Python traceback.  
  

> open "/Users/tianyizhang98/Princeton Dropbox/Tianyi
> Zhang/Computations/Borylation
> Computation/(ACNC)Fe/iPrACNCFeBPin2/singlet/opt/iPrACNCFeBpin2_singlet_opt_tpss-
> tzvp.out"

Summary of feedback from opening /Users/tianyizhang98/Princeton Dropbox/Tianyi
Zhang/Computations/Borylation
Computation/(ACNC)Fe/iPrACNCFeBPin2/singlet/opt/iPrACNCFeBpin2_singlet_opt_tpss-
tzvp.out  
---  
error | unable to open iPrACNCFeBpin2_singlet_opt_tpss-tzvp.out as a ORCA output file  
warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out   
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
an error occured while reading the ORCA output file  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
  
2 messages similar to the above omitted  
  
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/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
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 605,
in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/SEQCROW/io.py", line 46, 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
1634, 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
3280, in read_orca_out  
raise e  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2720, in read_orca_out  
raise e  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2712, in read_orca_out  
gradient.append([float(x) for x in info[3:]])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2712, in <listcomp>  
gradient.append([float(x) for x in info[3:]])  
^^^^^^^^  
ValueError: could not convert string to float: '0.0Starting'  
  
ValueError: could not convert string to float: '0.0Starting'  
  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2712, in  
gradient.append([float(x) for x in info[3:]])  
^^^^^^^^  
  
See log for complete Python traceback.  
  

> open "/Users/tianyizhang98/Princeton Dropbox/Tianyi
> Zhang/Computations/Borylation
> Computation/(ACNC)Fe/iPrACNCFeBPin2/singlet/opt/iPrACNCFeBpin2_singlet_opt_tpss-
> tzvp.out"

Summary of feedback from opening /Users/tianyizhang98/Princeton Dropbox/Tianyi
Zhang/Computations/Borylation
Computation/(ACNC)Fe/iPrACNCFeBPin2/singlet/opt/iPrACNCFeBpin2_singlet_opt_tpss-
tzvp.out  
---  
error | unable to open iPrACNCFeBpin2_singlet_opt_tpss-tzvp.out as a ORCA output file  
warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out   
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
an error occured while reading the ORCA output file  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = iPrACNCFeBpin2_singlet_opt_tpss-tzvp.inp  
| 1> ! RKS Opt TPSS D4 RIJCOSX DKH-def2-TZVP def2/J def2-TZVP/C Freq  
TightOpt TightSCF  
| 2>  
| 3> %base "iPrACNCFeBpin2_singlet_opt_tpss-tzvp"  
| 4>  
| 5> %SCF  
| 6> MaxIter 5000  
| 7> end  
| 8>  
| 9> * xyzfile 0 1 iPrACNCFeBpin2-guessgeom.xyz # S=0, 5-coord d6 Fe(II)  
| 10>  
| 11> %pal nprocs 16 end  
| 12>  
| 13> %maxcore 8000  
| 14>  
| 15> %output  
| 16> Print[P_Basis] 2  
| 17> Print[P_MOs] 1  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
error while reading ORCA gradient  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
data read:  
[]  
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: 1 C : 0.0Starting D4  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, 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,  
energy_context, forces, gradient  
  
2 messages similar to the above omitted  
  
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 605,
in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/SEQCROW/io.py", line 46, 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
1634, 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
3280, in read_orca_out  
raise e  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2720, in read_orca_out  
raise e  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2712, in read_orca_out  
gradient.append([float(x) for x in info[3:]])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2712, in <listcomp>  
gradient.append([float(x) for x in info[3:]])  
^^^^^^^^  
ValueError: could not convert string to float: '0.0Starting'  
  
ValueError: could not convert string to float: '0.0Starting'  
  
File "/Users/tianyizhang98/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/AaronTools/fileIO.py", line
2712, in  
gradient.append([float(x) for x in info[3:]])  
^^^^^^^^  
  
See log for complete Python traceback.  
  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.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
      Model Number: MGND3LL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 18 days, 19 hours, 49 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      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 22cwa:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          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: 1.9.7
    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

[Eric Pettersen]

Reported by Tianyi Zhang

[Tony Schaefer]

Tianyi Zhang,

Thanks for reporting this. I'm not able to reproduce this with my version
of orca 6.1. It looks like some things might have been printed to the file
in the wrong order. Are you able to send me the file?

Best,

Tony

On Mon, Apr 6, 2026 at 2:04 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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